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Zhang, Mei. "Cross-docking network design." Diss., Georgia Institute of Technology, 1997. http://hdl.handle.net/1853/21685.
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Iakovou, Georgios. "Simulating molecular docking with haptics." Thesis, University of East Anglia, 2015. https://ueaeprints.uea.ac.uk/59468/.
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Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process. In molecular docking, haptics enables the user to sense the interaction forces and intervene cognitively in the docking process. Haptics-assisted docking systems provide an immersive virtual docking environment where the user can interact with the molecules, feel the interaction forces using their sense of touch, identify visually the binding site, and guide the molecules to their binding pose. Despite a forty-year research e�ort however, the docking community has been slow to adopt this technology. Proprietary, unreleased software, expensive haptic hardware and limits on processing power are the main reasons for this. Another signi�cant factor is the size of the molecules simulated, limited to small molecules. The focus of the research described in this thesis is the development of an interactive haptics-assisted docking application that addresses the above issues, and enables the rigid docking of very large biomolecules and the study of the underlying interactions. Novel methods for computing the interaction forces of binding on the CPU and GPU, in real-time, have been developed. The force calculation methods proposed here overcome several computational limitations of previous approaches, such as precomputed force grids, and could potentially be used to model molecular exibility at haptic refresh rates. Methods for force scaling, multipoint collision response, and haptic navigation are also reported that address newfound issues, particular to the interactive docking of large systems, e.g. force stability at molecular collision. The i ii result is a haptics-assisted docking application, Haptimol RD, that runs on relatively inexpensive consumer level hardware, (i.e. there is no need for specialized/proprietary hardware).
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Atkovska, Kalina, Sergey A. Samsonov, Maciej Paszkowski-Rogacz, and M. Teresa Pisabarro. "Multipose Binding in Molecular Docking." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-147177.
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Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.
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Huggins, David John. "Multiscale docking using evolutionary optimisation." Thesis, University of Oxford, 2005. http://ora.ox.ac.uk/objects/uuid:f166d5ec-5085-48b9-838a-626f754f73fb.
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Molecular docking algorithms are computational methods that predict the binding site and docking pose of specified ligands with a protein target. They have proliferated in recent years, due to the explosion of structural data in biology. Oxdock is an algorithm that uses various techniques to simplify this complex task, the most significant being the use of a multiscale approach to analyse the problem using a simple representation in the early stages. Oxdock is shown to be a very useful tool in computational biology, as exemplified by two cases. The first case is the analysis of the NMDA subclass of neuronal glutamate receptors and the subsequent elucidation of their function. The second is the investigation of the newly discovered plant glutamate receptors and the clarification of their natural ligands. The results in both instances open new areas of research into exciting areas of biology. Despite its effectiveness in solving many problems, Oxdock does fail in a number of circumstances. It is thus important to devise a new and improved method for molecular docking. This is achieved by combining the speed of the multiscale approach with the optimising ability of Evolutionary Programming. This yields an algorithm that is shown to be precise, accurate and specific. The new algorithm, Eve, is then modified to illustrate its potential in both lead optimisation and de novo drug design. These capacities, combined with its ability to predict the location of binding sites and the docking pose of a ligand, highlight the promise of computational methods in solving problems in many areas of biological chemistry.
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Ремыга, Ю. С. "Технология cross-docking – особенности применения." Thesis, Национальный авиационный университет, 2010. https://er.nau.edu.ua/handle/NAU/46688.
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Кросс-докинг представляет собой логистическую технологию, при которой разгрузка товара внутри склада и его последующая доставка получателю максимально согласованы по времени. Это позволяет практически полностью устранить из цепи поставок складское хранение. Таким образом, кросс-докинг — реальная возможность существенно снизить расходы на складскую логистику.
Основное преимущество кросс-докинга заключается в существенной экономии логистических затрат: практически устраняются затраты на хранение товара, снижается потребность организации-грузополучателя в складских площадях и складском персонале, отсутствие складского хранения значительно сокращает время поставки от производителя до конечной точки продажи, что повышает скорость товаропотока. Это особенно актуально для товаров, имеющих ограниченный срок годности, исчисляемый несколькими сутками, поскольку при формировании крупных партий на складе по завершении срока реализации, присутствуют остатки, являющиеся прямыми потерями. При использовании кросс-докинга заказы для поставщика формируются строго под потребности конечного покупателя. В результате нет потерь по срокам годности и нет затоваривания.
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BOCZAR, LUDVIG, and JONATHAN PERNOW. "Autonomous Docking of Electric Boat." Thesis, KTH, Skolan för industriell teknik och management (ITM), 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-299765.
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In recreational boating, docking is one of the most stressful and accident prone situations. Due to the loss of maneuverability at low speeds, it is a procedure that requires experience. There are mainly two problems when it comes to autonomous docking of a boat, these are identifying a berth’s position as well as keeping the boat on its intended path and correcting any deviations. Autonomous docking in recreational boating is still quite uncommon, with companies still exploring different solutions. This thesis proposes a Model Predictive Control (MPC) system combined with Pulsed Coherent Radar technology, equipped on an under-actuated boat model, to achieve autonomous docking. A major part of this thesis was to evaluate the amount and placement of radar sensors, as well as determining whether these are suitable in a water environment. In order to test this, the sensors were placed alongside the hull of the boat. It was found that the placement of sensors had a bigger impact than the amount when it came to correctly detecting the position of a berth. Once the placement of sensors and the berth position algorithmhad been done, a closed-loop MPC was used. This controller got constant feedback of the boat’s position relative the berth, in order to calculate the thruster control inputs for the next time step. The developed autonomous docking system was then implemented on the boat which was tested in a swimming pool. The optimal radar configuration combined withMPC, made it possible to successfully dock a boat autonomously without any modification to the berth.För fritidsbåtlivet är tilläggning en av demest stressfulla och olycksbenägna situationerna. På grund av förlust av manövrering vid låga hastigheter är det en procedur som kräver erfarenhet. Det finns främst två problem när det kommer till autonom tilläggning, det är att identifiera positionen av en brygga såväl som att hålla båten på den avsedda kursen och rätta till små avvikelser. Autonom tilläggning för fritidsbåtlivet är fortfarande rätt ovanligt och företag utforskar fortfarande olika lösningar. Denna avhandling föreslår ett Modellprediktivt Reglersystem (MPC) kombinerat med Pulserad Koherent Radarteknik som är utrustad på en underaktuerad båtmodell för att uppnå autonom tilläggning. En stor del av avhandlingen var att utvärdera antalet och placeringen av radarsensorer, såväl som att fastställa om dessa är lämpliga att användas i en vattenmiljö. För att undersöka detta placerades sensorerna längs med båtens skrov. Det konstaterades att placeringen av sensorer hade en större påverkan än mängden när det kom till att läsa av positionen av bryggan korrekt. När placeringen av sensorer och bryggpositionsalgoritmen var klar användes MPC med återkoppling. Denna regulator fick konstant återkoppling av båtens position relativt bryggan för att räkna ut styrsignal till motorerna för nästa tidssteg. Den utvecklade autonoma tilläggningen var sedan implementerad på båten som testades i en pool. Den optimala radarplaceringen kombinerat med MPC gjorde det möjligt att med framgång kunna lägga till båten autonomt utan modifiering av bryggan.
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Švehlová, Zuzana. "Cross-docking ako distribučná metóda." Master's thesis, Vysoká škola ekonomická v Praze, 2010. http://www.nusl.cz/ntk/nusl-73809.
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The current logistics chains must be designed to copy with short life cycles of products, high stock velocity, low degree of predictability etc. The conditions for accuracy, reliability and flexibility of deliveries at the markets have been changing, and that is why it is inevitable to seek new alternative methods that would lead to higher efficiency levels, remaining competitiveness and, at the same time, fulfil the needs and wishes of customers. In this paper I focuse on cross-docking which is a newer distribution method. In the first part of the paper, I try to determine the principles of this operation in distribution, identify individual types of cross-docking and in detail describe the assumptions and conditions under which the method should be implemented to reach the requested results. The paper then continues with an analysis of the current position of cross-docking and there are given several examples of demand driven supply chains that have been using this distribution method at a certain point. These examples are followed with a discussion on current options and problems of implementing cross-docking in the case of retailers and manufacturers.
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Zöllner, Frank G. "Enhancing protein-protein docking by new approaches to protein flexibility and scoring of docking hypotheses." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972854142.
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Genheden, Samuel. "A fast protein-ligand docking method." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-69.
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In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biological feasibility. The method was evaluated on a set of 310 protein-ligand complexes. The results show that with respect to docking the method with its initial parameter settings is too coarse grained. The results also show that with respect to ranking of putative active sites the method works quite well.
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Thörn, Victor. "Cross-docking i teori och praktiken." Thesis, Mälardalens högskola, Innovation och produktrealisering, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:mdh:diva-37251.
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Eatherley, Graham J. "Autonomous vehicle docking using fuzzy logic." Thesis, University of Ottawa (Canada), 1994. http://hdl.handle.net/10393/6731.
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Autonomous control of robot vehicles has been studied recently by AI researchers with simulations and implementations emerging using both Neural Networks and Fuzzy Systems. The application is important primarily for autonomous control of planetary surface rovers and deep space vehicles where telepresence control (remote human operator) is precluded because of the long signal transit time. The problem of vehicle docking is specifically addressed in this thesis and the results of experiments on a small model truck and trailer using a mechanical based position sensing systems is reported. Fuzzy logic controls both forward and backward motion of the vehicle to successfully dock the trailer. Additionally, it is shown how the position sensing system can be improved using a small laser-based bar code engine. Future research including use of the system on other mobile robot platforms is discussed and we describe other research planned for the platform. In this thesis the author shows that the use of fuzzy logic for vehicle control simplifies the analysis of motion required to produce proper docking. In particular, the discontinuity of control produced by switching from forward to reverse is readily handled by fuzzy logic.
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Taylor, Richard David. "Novel simulation methods for flexible docking." Thesis, University of Southampton, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368873.
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Totrov, Maxim. "Computational studies on protein-ligand docking." Thesis, Open University, 1999. http://oro.open.ac.uk/58005/.
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This thesis describes the development and refinement of a number of techniques for molecular docking and ligand database screening, as well as the application of these techniques to predict the structures of several protein-ligand complexes and to discover novel ligands of an important receptor protein. Global energy optimisation by Monte-Carlo minimisation in internal co-ordinates was used to predict bound conformations of eight protein-ligand complexes. Experimental X-ray crystallography structures became available after the predictions were made. Comparison with the X-ray structures showed that the docking procedure placed 30 to 70% of the ligand molecule correctly within 1.5A from the native structure. The discrimination potential for identification of high-affinity ligands was derived and optimised using a large set of available protein-ligand complex structures. A fast boundary-element solvation electrostatic calculation algorithm was implemented to evaluate the solvation component of the discrimination potential. An accelerated docking procedure utilising pre-calculated grid potentials was developed and tested. For 23 receptors and 63 ligands extracted from X-ray structures, the docking and discrimination protocol was capable of correct identification of the majority of native receptor-ligand couples. 51 complexes with known structures were predicted. 35 predictions were within 3A from the native structure, giving correct overall positioning of the ligand, and 26 were within 2A, reproducing a detailed picture of the receptor-ligand interaction. Docking and ligand discrimination potential evaluation was applied to screen the database of more than 150000 commercially available compounds for binding to the fibroblast growth factor receptor tyrosine kinase, the protein implicated in several pathological cell growth aberrations. As expected, a number of compounds selected by the screening protocol turned out to be known inhibitors of the tyrosine kinases. 49 putative novel ligands identified by the screening protocol were experimentally tested and five compounds have shown inhibition of phosphorylation activity of the kinase. These compounds can be used as leads for further drug development.
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Andersson, Oscar, and Lucas Molin. "AutoTruck : Automated docking with internal sensors." Thesis, KTH, Maskinkonstruktion (Inst.), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-230383.
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The purpose of this bachelor thesis was to discover howan articulated vehicle can park itself using a pre-definedparking path with a combination of ultrasonic sensors aswell as a rotary angle sensor.The project was divided into two parts: constructing asmall scale demonstrator and the software controlling thedemonstrator. The demonstrator was constructed from offthe-shelf components and custom parts. The truck was designedbased on a rear wheel driven truck with Ackermannsteering. The localization of a parking spot and measuringother distances was done with ultrasonic sensors and thehitch angle was measured by a rotary angle sensor.The performance of the demonstrator was evaluated bymeasuring the trailers angle difference from the center lineof the parking spot.The performance was deemed to be reasonably goodwith successful parkings in 8 out of 10 attempts.Kandidatarbetet syftar till att undersöka hur ett ledatfordon kan parkera sig självt efter en förbestämd parkeringsruttmed en kombination av flera ultraljudssensorersamt en vinkelgivare.Projektet består av två delar; konstruktion av ett miniatyrfordonsamt mjukvaran som styr fordonet. Fordonettillverkades från butiksköpta komponenter och skräddarsyddadelar. Lastbilens design var baserad p°a en bakhjulsdrivenAckermannstyrd lastbil. Identifieringen av en parkeringsplatssamt avståndsmätning hanterades av ultraljudssensoreroch hitch vinkeln mättes av en vinkelgivare.Miniatyrfordonets prestanda utvärderades genom attmäta släpets vinkelskillnad från centerlinjen av parkeringsplatsen.Prestandan ansågs att vara tillräckligt god med lyckadeparkeringar i 8 av 10 tester.
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Luo, Gaohao Noble James S. "An integrated model of cross docking." Diss., Columbia, Mo. : University of Missouri--Columbia, 2008. http://hdl.handle.net/10355/6280.
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Title from PDF of title page (University of Missouri--Columbia, viewed on Feb. 18, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dr. James S. Noble, Thesis Supervisor. Includes bibliographical references.
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Mirzaei, Hanieh. "Manifold optimization methods for macromolecular docking." Thesis, Boston University, 2014. https://hdl.handle.net/2144/11149.
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Thesis (Ph.D.)--Boston UniversityThis thesis develops efficient algorithms for local optimization problems encountered in predictive docking of biological macromolecules. Predictive docking, defined as computationally obtaining a model of the bound complex from the coordinates of the two component molecules, is one of the fundamental and challenging problems in computational structural biology. Docking methods generally search for the minima of an energy or scoring function that estimates the binding free energy or, more frequently, the interaction energy, of the two molecules. These energy functions generally have large numbers of local minima, resulting in extremely rugged energy landscapes. Therefore, independently of the algorithm used for sampling the conformational space, virtually all docking algorithms include some type of local continuous minimization of the energy function. Most state-of-the-art algorithms allow for the free movement of all atoms of the two molecules and rely on the minimization of the energy function to enforce structural constraints of the molecules. In contrast this thesis exploits the partial or complete rigidity of the molecules when defining the conformational space. As a result, the local optimization problems are formulated as optimization problems on appropriately defined manifolds. In the case of rigid docking, a novel manifold representation of rigid motions of a body is introduced that resolves many of the optimization difficulties associated with the commonly used manifold for this purposed , the so-called Special Euclidean group, SE(3). These difficulties arise from a coupling that SE(3) introduces between the rotational and translational move of the body. The new representation decouples these moves and results in a more appropriate and flexible optimization algorithm. Experimental results show that the proposed algorithm is an order of magnitude more efficient than the current state-of-the-art algorithms. The proposed manifold optimization approach is then extended to the case of flexible docking. The novel manifold representation of rigid motions is combined with the so-called internal coordinate representation of flexible moves to define a new manifold to which the original manifold optimization algorithm can be directly extended. Computational results show that the resulting optimization algorithm is substantially more efficient than energy minimization using a traditional all-atom optimization algorithm while producing solutions of comparable quality. It is shown that the application of the proposed local optimization algorithm as one of the components of a multi-stage refinement protocol for protein-protein docking contributes significantly to the refinement stage by helping to move the distribution of docking decoys closer to the corresponding bound structures. Finally, it is shown that the approach of the thesis can be substantially generalized to address the problem of minimization of a cost function that depends on the location and poses of one or more rigid bodies, or bodies that consist of rigid parts hinged together. This is a formulation used in a number of engineering applications other than molecular docking.
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ANDERSSON, OSCAR, and LUCAS MOLIN. "AutoTruck : Automated docking with internal sensors." Thesis, KTH, Mekatronik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-233142.
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The purpose of this bachelor thesis was to discover how an articulated vehicle can park itself using a pre-defined parking path with a combination of ultrasonic sensors as well as a rotary angle sensor. The project was divided into two parts: constructing a small scale demonstrator and the software controlling the demonstrator. The demonstrator was constructed from offthe- shelf components and custom parts. The truck was designed based on a rear wheel driven truck with Ackermann steering. The localization of a parking spot and measuring other distances was done with ultrasonic sensors and the hitch angle was measured by a rotary angle sensor. The performance of the demonstrator was evaluated by measuring the trailers angle difference from the center line of the parking spot. The performance was deemed to be reasonably good with successful parkings in 8 out of 10 attempts.Kandidatarbetet syftar till att undersöka hur ett ledat fordon kan parkera sig självt efter en förbestämd parkeringsrutt med en kombination av flera ultraljudssensorer samt en vinkelgivare. Projektet består av två delar; konstruktion av ett miniatyrfordon samt mjukvaran som styr fordonet. Fordonet tillverkades från butiksköpta komponenter och skräddarsydda delar. Lastbilens design var baserad på en bakhjulsdriven Ackermannstyrd lastbil. Identifieringen av en parkeringsplats samt avståndsmätning hanterades av ultraljudssensorer och hitch vinkeln mättes av en vinkelgivare. Miniatyrfordonets prestanda utvärderades genom att mäta släpets vinkelskillnad från centerlinjen av parkeringsplatsen. Prestandan ansågs att vara tillräckligt god med lyckade parkeringar i 8 av 10 tester.
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Johansson, Tim, and Pontus Nilsson. "Further Development of a Docking Station : Redesign of MagniLink S Docking Station at LVI Low Vision International." Thesis, Linnéuniversitetet, Institutionen för maskinteknik (MT), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-44186.
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The purpose of this work is to evaluate how a docking station can be more future proof, environmentally friendly and satisfy the customers’ needs more. The docking station in focus of this project is owned by LVI, and used with one of their cameras MagniLink S. When comparing the results of the new docking station and the current docking station, the new docking station is more future proof, environmentally friendly and satisfies the customers’ needs more. In the end it is established that following steps should be followed during the development of a docking station: - Make sure that the cables are reliably fastened into the docking station and that the connectors can handle the docking force. - Design to use more material with lower environmental impact and ensure that the material fulfils the product requirements and objectives. Use as small amount of material as possible. - Prioritize the customers’ expressed and unexpressed needs as one of the highest priorities during the development process.
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Loberg, Jon-Erik. "Planar Docking Algorithms for Underactuated Marine Vehicles." Thesis, Norwegian University of Science and Technology, Department of Engineering Cybernetics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-10039.
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The use of autonomously underwater vehicles (AUVs) has a great potential in scientific mission involving underwater exploration. However a major drawback with todays AUV missions is the launch and recovery process which are usually performed manually from a manned supply ship. These manned ships have a huge daily operation cost, and because AUVs can have operation times up to 70 hours these missions become extremely costly. Since the combination of an AUV together with a manned mothership is very costly the use of AUVs are very restricted. A solution here is to replace the manned mothership with an unmanned vehicle such as a unmanned surface vehicle (USV). This will reduce the cost of AUV mission drastically and therefore increase the use of AUVs on scientific missions. This motivates the need for an AUV-USV docking method which is one of the two docking scenarios treated in this master thesis. Another docking method treated here is the possibility to dock a USV together with a manned mothership without human interference. A docking method that removes the human intervention will make the USV completely unmanned, since USVs today are manually docked together with a mothership or driven back to shore by a remote control. To achieve an understanding of the field, a summary of the most relevant findings in todays literature are given. This includes the possibility to autonomously dock together an AUV with another vehicle or installation, and other related fields such as spacecraft docking and aerial refuelling. The main findings involving AUV docking, ranges from a simple fuzzy logic procedure to more advanced methods involving trajectory planning and potential field guidance. Since no extensive previous work exist on general USV docking, a short introduction is given to the most related fields, such as spacecraft docking and aerial refuelling. During air refuelling two methods are summarised which includes racetrack pattern or waypoint paths, where the receiver aircraft has two different ways of rendezvousing with the tanker, namely point parallel- or route-rendezvous. In both docking scenarios treated here, rendezvous guidance is developed since the vehicles are assumed underactuated. The docking procedure is divided into two stages, a homing stage and a docking stage. In the homing stage only rough guidance is needed which is not the case during docking stage where requirements are much tighter on positioning to avoid collisions. In the AUV to USV homing stage the USV does all the work, but during docking stage the AUV has full responsibility, since the USV only traverses along a straight path. The USV's path is here orientated against the wind direction to minimise the sideslip effect caused due to weather disturbances. Once the USV has converged to a straight path the AUV proceeds to docking from behind the USV to finalise docking. For the USV to mothership docking scenario, the USV has the full responsibility during the whole docking procedure. Here the USV is underactuated, and therefore the mothership will be in motion and only has to avoid sudden manoeuvres. In the homing stage the USV will manoeuvre towards a point given on the line of sight vector between the two vehicles. Once the USV reaches this point it will steer along a circle around the mothership to avoid collisions and to position itself in clear sight of the docking point. With clear sight achieved the USV will use its forward motion to converge sideways towards the docking point, such that docking can be completed. Finally, simulations are carried out to verify the behaviour of the developed guidance laws. During these simulations two 3DOFs underactuated USV models are being used, where both vehicles only has controllability over surge speed and yaw rate. In both docking scenarios the whole docking procedure is analysed including homing and docking stage. The simulation results shows a proper docking with a satisfying approach in both scenarios. Also the mothership's velocity is examined to understand the USV's sideway approach towards the mothership.
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Wang, Chu. "Improved conformational sampling for protein-protein docking /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9194.
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Claußen, Holger. "Effizientes Protein-Ligand-Docking mit flexiblen Proteinstrukturen /." Sankt Augustin : GMD-Forschungszentrum Informationstechnik, 2001. http://www.gbv.de/dms/bs/toc/33264023X.pdf.
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Oledzki, Peter Richard. "Developing a protein-ligand docking algorithm : FlexLigDock." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.435818.
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Seito, Narumi. "Modelagem e simulação de rendezvous e docking." Instituto Nacional de Pesquisas Espaciais (INPE), 2015. http://urlib.net/sid.inpe.br/mtc-m21b/2015/06.03.14.07.
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Esta tese tem como objetivo apresentar uma solução para o problema de RVD/B (encontro e acoplamento/atracação) entre duas espaçonaves, perseguidora e alvo, em órbita. Depois de uma breve revisão da literatura para contextualizar este trabalho, apresentam-se as estratégias de aproximação, as técnicas de sincronização de órbita e atitude, e a técnica de aproximação de proximidade, sendo suportadas por dois sistemas de equações diferenciais para os movimentos translacional e rotacional das espaçonaves. Duas configurações são consideradas para a espaçonave robótica perseguidora: uma, quando o manipulador robótico, nela incorporado, estiver inerte, e a outra, quando o manipulador robótico estiver em ação. Na primeira configuração, a formulação newtoniana é usada para obter as equações da dinâmica de translação de Hill-Clohessy-Wiltshire, e o movimento de atitude é determinado pelas equações de Euler. Estes dois sistemas de equações obtidos acima permitem conduzir o perseguidor até o espaço de trabalho de atracação do alvo. Na segunda configuração, a formulação de Lagrange, para quase-coordenadas e para coordenadas generalizadas, fornece as equações do movimento do manipulador robótico para a atracação no alvo. No equacionamento e na simulação numérica das aberturas do manipulador robótico, reside a originalidade da tese. As simulações computacionais da dinâmica de ambas as configurações foram implementadas utilizando-se o pacote de software MatLab.In this thesis strategies to solve the problem of the RVD/B (RendezVous and Docking/Berthing) orbital operations are studied. In a brief review of the literature, the strategies of approximation, the techniques for orbit and attitude synchronization, and the technique for the close proximity approximation are presented, all of them supported by two systems of differential equations for the translational and rotational motion of both spacecrafts. Two configurations are considered for the chaser: one when the robotic manipulator of the chaser is inert, and a second one when the robotic manipulator is in action. In the first configuration the Newtonian formulation is used to obtain the equations of Hill-Clohessy-Klein for the translational dynamics, while the attitude motion is determined by Eulers equations. These two systems of differential equations allow to guide the chaser up to the point for berthing the target. In the second configuration, the Lagrangian formulation for quasi-coordinates and generalized coordinates supplies the equations for the motion of the robotic manipulator when berthing the target. These latter equations and their numerical simulation of berthing the target are the original part of this thesis. The computational simulations of the dynamics are carried out by use of the software MatLab.
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Whiteley, Chris G., C.-Y. Shing, C.-C. Kuo, and Duu-Jong Lee. "Docking of HIV protease to silver nanoparticles." Elsevier, 2016. http://hdl.handle.net/10962/67105.
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publisher versionThis interaction of silver nanoparticles (AgNP) with human immune-deficiency virus aspartic protease (HIVPR) is examined by molecular dynamics simulation using the Colores (Situs) package and biophysical techniques using UV–vis spectroscopy, dynamic light scattering, transmission electron microscopy and circular dichroism. The ‘docking’ of AgNP with HIVPR creates a complex [AgNP–HIVPR] to initiate a hypochromic time-dependent red-shift for the surface plasmon resonance maximum. MD simulations reflect large perturbations to enzyme conformations by fluctuations of both rmsd and B-factors. Increase in changes to electrostatic potentials within the enzyme, especially, with chain B, suggest hydrophobic interactions for the binding of the AgNP. This is supported by changes to mainchain and sidechain dihedrals for many hydrophobic amino acid including Cys95, Trp6 and Trp42. Circular dichroism spectra reveal disappearance of α-helices and β-sheets and increase in random coil first from chain B then chain A. During initial stages of the interactive simulation the enzyme is conformational flexible to accommodate the AgNP, that docks with the enzyme under a cooperative mechanism, until a more stable structure is formed at convergence. There is a decrease in size of the HIVPR–AgNP complex measured by changes to the gyration radius supporting evidence that the AgNP associates, initially, with chain B.
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Huang, Bingding. "Improving protein docking with binding site prediction." Doctoral thesis, [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1216305428189-09951.
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Duzzi, Matteo. "Spacecraft Rendezvous and Docking Using Electromagnetic Interactions." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3422295.
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On-orbit operations such as refuelling, payload updating, inspection, maintenance, material and crew transfer, modular structures assemblies and in general all those processes requiring the participation of two or more collaborative vehicles are acquiring growing importance in the space-related field, since they allow the development of longer-lifetime missions.
To successfully accomplish all these on-orbit servicing operations, the ability to approach and mate with another vehicle is fundamental. Rendezvous strategies, proximity procedures and docking manoeuvres between spacecraft are of utmost importance and new, effective, standard and reliable solutions are needed to ensure further technological developments.
Presently, the possibility to create low-cost clusters of vehicles able to share their resources may be exploited thanks to the broadening advent of CubeSat-sized spacecraft, which are conditioning the space market nowadays.
In this context, this thesis aims at presenting viable strategies for spacecraft RendezVous and Docking (RVD) manoeuvres exploiting electro-magnetic interactions. Two perspective concepts have been investigated and developed, linked together by the use of CubeSat-size testing platforms.
The idea behind the first one, PACMAN (Position and Attitude Control with MAgnetic Navigation) experiment, is to actively exploit magnetic interactions for relative position and attitude control during rendezvous and proximity operations between small-scale spacecraft. PACMAN experiment has been developed within ESA Education Fly Your Thesis! 2017 programme and has been tested in low-gravity conditions during the 68th ESA Parabolic Flight Campaign (PFC) in December 2017. The experiment validation has been accomplished by launching a miniature spacecraft mock-up (1 U CubeSat, the CUBE) and a Free-Floating Target (1 U CubeSat, the FFT) that generates a static magnetic fields towards each other; a set of actively-controlled magnetic coils on board the CUBE, assisted by dedicated localization sensors, are used to control the CUBE attitude and relative position, assuring in this way the accomplishment of the soft-docking manoeuvre.
The second one, TED (Tethered Electromagnetic Docking), concerns a novel docking strategy in which a tethered electromagnetic probe is expected to be ejected by a chaser toward a receiving electromagnetic interface mounted on a target spacecraft. The generated magnetic field drives the probe to the target and realizes an automatic alignment between the two interfaces, thus reducing control requirements for close approach manoeuvres as well as the fuel consumption necessary for them. After that, hard-docking can be accomplished by retracting the tether and bringing the two spacecraft in contact.La capacità di eseguire operazioni di servizio su veicoli in orbita ha riscontrato, negli ultimi anni, un’enorme interesse da parte delle maggiori compagnie e agenzie spaziali internazionali. La necessità di ridurre i costi di produzione, assieme alla possibilità di ottenere sistemi complessi più affidabili e duraturi, ha indirizzato marcatamente il mercato dell’ingegneria aerospaziale verso lo studio di soluzioni innovative per eseguire in orbita operazioni quali rifornimento, aggiornamento e manutenzione di sottositemi, riparazioni di componenti non funzionanti e ispezioni. Le nuove idee e tecnologie in via di sviluppo per eseguire queste operazioni sono percepite come estremamente funzionali e efficienti in termini di costo, in grado di estendere la vita operativa di un satellite e diminuire i costi connessi alla sua completa sostituzione. Attualmente, il tassello mancante per poter procedere efficacemente con questo tipo di procedure, è un sistema automatico di docking che possa costituire un nuovo standard semplice ed affidabile. Gli odierni sistemi di docking, infatti, sono caratterizzati da elevati requisiti di puntamento e necessitano dell’attuazione di precise azioni sul controllo d’assetto in modo da garantire un aggancio sicuro tra i due veicoli coinvolti nella manovra. Questo è dovuto al fatto che tali sistemi di aggancio sono stati progettati quasi unicamente per il trasferimento di equipaggio o di materiali mentre nessuna progettazione, finora, è mai stata prevista per i satelliti commerciali e scientifici. Recentemente, l’avvento dei CubeSat ha fortemente incoraggiato aziende e agenzie del settore aerospaziale ad investire nello sviluppo di dimostratori tecnologici e payload scientifici, grazie alla notevole riduzione nel costo necessario per lanciare in orbita tali veicoli. Lo svantaggio nell’utilizzare questo tipo di piattaforme è principalmente legato ai limiti tecnici intrinseci degli stessi, rappresentati dalle ridotte risorse a disposizione. Ciononostante, gran parte di queste limitazioni sono state superate grazie alla possibilità di scalare i risultati ottenuti ed applicarli a sistemi più grandi. Numerose tecnologie sono già state testate e caratterizzate nello spazio usando moduli CubeSat, ma solo esperimenti marginali sono stati condotti sino ad oggi su sistemi di docking, anche se si sta percependo un cambio di tendenza. Tali sistemi, infatti, permetterebbero l’esecuzione di operazioni di aggancio e sgancio, ampliando enormemente i possibili scenari di missione: sistemi modulari formati da molteplici unità CubeSat potrebbero interagire tra loro creando agglomerati più grandi in grado di condividere le risorse più efficacemente, riorganizzarsi e aggiornarsi autonomamente. Lo scopo di questa ricerca è quello di proporre un nuovo sistema di soft-docking caratterizzato da requisiti meno stringenti per quanto concerne l’accuratezza nel puntamento e nel controllo d’assetto rispetto ai sistemi esistenti. L’idea innovativa alla base dello studio è quella di sfruttare la capacità di auto-allineamento e reciproca attrazione garantita dall’interazione magnetica che si instaura tra due interfacce elettromagnetiche, in modo da facilitare le manovre di prossimità ed aggancio. La trattazione è suddivisa in due parti principali. Nella prima parte viene presentato l’esperimento PACMAN (Position and Attitude Control with MAgnetic Navigation) il quale rappresenta un dimostratore tecnologico di un sistema di docking per piccoli satelliti basato su attuatori magnetici. Tale sistema, sviluppato all'interno del programma ESA Education Fly Your Thesis! 2017, è stato testato in gravità ridotta durante la 68th campagna di voli parabolici ESA a dicembre. La seconda parte si focalizza invece su un nuovo concept, TED (Tethered Electromagnetic Docking), secondo il quale le manovre di close-range rendezvous e docking possono essere realizzate lanciando una sonda elettromagnetica collegata ad un filo da un satellite chaser verso un’interfaccia elettromagnetica montata su di un satellite target. Stabilito il collegamento, tramite il recupero del filo, i due veicoli sono connessi rigidamente concludendo la manovra.
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Saladin, Adrien. "Macromolecular Docking : applications to the RecA nucleofilament." Paris 7, 2009. http://www.theses.fr/2009PA077098.
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Les protéines jouent un rôle central dans de nombreux processus cellulaire et peuvent intervenir dans de nombreuses interactions différentes, avec d'autres protéines, de l'ADN, des lipides, ou de petits ligands. La détermination de ces interactions est fondamentale pour pouvoir comprendre des processus biologiques majeurs et de nombreuses méthodes expérimentales ont été développées pour les caractériser. Cependant les méthodes expérimentales sont longues et coûteuses et les méthodes informatisées de prédictions d'interactions pourraient, à terme, fournir dans ce contexte une aide précieuse permettant de guider de futures expériences en biochimie et biologie moléculaire. Le développement logiciels d'amarrage est également un processus difficile mettant en jeu des cycles de conception d'algorithme, d'implémentation et de tests. Au cours de ma thèse, j'ai développé une librairie orientée objet pour favoriser et accélérer les étapes d'implémentation et de tests des méthodes d'amarrage. Cette librairie, programmée en C++ et interfacée avec le langage de script Python, a été utilisée pour mettre au point et tester de nouvelles méthodes appliquées à l'amarrage protéine-ADN et à l'amarrage multi-composants. Des programmes développés à l'aide de cette librairie sont actuellement appliqués à l'étude des modes d'amarrage de l'ADN au complexe RecA, responsable de la recombinaison homologue chez les bactériesProteins play a central role in various cellular processes with various interactions with other proteins, DNA, lipids or small ligands. Because the determination of these interactions is fundamental for understanding key biological processes, several experimental methods have been developed to characterize them. Experimental studies can take a long time and an expensive. Computational methods can therefore be of great help to guide future biochemical experiments. Development of docking software is a long process involving cycles of algorithm conception, programming and tests. During my thesis, I developed an object oriented library to help and speed-up development and tests of docking methods. This library was programmed in C++ with Python bindings, and has been used to test new methods applied to protein-DNA docking and multicomponent docking. Programs made with the help of this library are presently used to study the binding of DNA to the RecA complex, responsible of homologous recombination
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Ferreira, Janaina Gomes. "Estudo de compostos quinônicos com potencial atividade contra a doença de Chagas." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/75/75131/tde-23062008-163355/.
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Este trabalho apresenta as estruturas determinadas por difração de raio X de dois compostos naftoquinônicos, 3,4-diidro-[2,2-dimetil]-2H-nafto[1,2-b]pirano-5,6-diona (β-lapachona) e dimetil-1,4-naftoquinona. A estrutura cristalina destes compostos mostrou que estes são estabilizados por ligações de hidrogênio do tipo C-H...O, formando estruturas supramoleculares. Dos compostos derivados da β-lapachona, os naftoimidazóis têm-se mostrado muito ativos contra o T. cruzi, agente causador da doença de Chagas. Partindo das estruturas modeladas de 29 compostos naftoimidazólicos, propriedades eletrônicas, geométricas e topológicas foram calculadas para análise estatística por mínimos quadrados parciais (PLS). Após a análise e redução das variáveis foram selecionados os descritores Morp17p, X4a, piPC09, RDF065v, BELp6, RDF060p, R4u, RDF035m e RCI que foram utilizados para a construção um modelo de regressão com o método de PLS. Para o modelo, o menor erro de validação foi obtido com 3 fatores e os coeficientes de correlação R= 0,71 e Q= 0,82. O estudo de docking de alguns compostos naftoquinônicos e naftoimidazólicos mostrou que, do ponto de vista energético e de complementaridade química, estes compostos possuem pouca probabilidade de se ligarem no sítio ativo da tripanotiona redutase (TR), uma enzima essencial para o metabolismo do T. cruzi, bem como no sítio ativo da enzima humana glutationa redutase (GR), homóloga a TR. Há, no entanto, uma tendência geral destes compostos se ligarem no sítio da interface, sobretudo, de se ligarem neste sítio da enzima humana.This work presents the structure determined by X-ray analyses for two naphthoquinone compounds 3,4-dihydro-2,2-dimethyl-2H-naphtho[1,2-b]pyran-5,6- dione and dimethyl-1,4-naphthoquinone. The crystal packing of these compounds showed the existence of intermolecular hydrogen bonds of the type CH...0. These intermolecular forces are responsible for the self-assembly in three-dimensional supramolecular structure. A set of 29 naphthoimidazoles, derived from β-lapachone, that has shown activity against T. cruzi, the agent of Chagas disease, were modeled. From these structures electronic, geometric, topological, etc, properties were calculated to be used in the investigation by statistic analysis, using the partial least squares method (PLS). After reduction of the number of variables, the best PLS model found was the one obtained with the following variables: Morp17p, X4a, piPC09, RDF065v, BELp6, RDF060p, R4u, RDF035m and RCI. For the PLS model, the lower error of validation was obtained using 3 factors with the coefficients R=0.71 and Q=0.82. Two sets of compounds, naphtoquinones and naphthoimidazoles, were studied by docking method. The results showed that, for both, naphtoquinones and naphthoimidazoles and both trypanothione and glutathione reductase, the compounds have low probability to bind in the active site, and are more likely to bind in the interface site, especially in the interface site of the human protein.
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Fischer, Bernhard Karl. "High throughput simulation methods for protein ligand docking." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/985070374/34.
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Sternberg, David Charles Ph D. Massachusetts Institute of Technology. "Optimal docking to tumbling objects with uncertain properties." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/112364.
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Thesis: Sc. D., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, 2017.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 227-242).
Active debris removal (ADR), on-orbit servicing and in-space assembly likely require proximity operations and soft docking between two or more satellites. These operations can be complicated by the presence of several challenges, including 1) flexible dynamics, 2) impending collision with other proximity objects, 3) uncooperative satellites, 4) tumbling behavior, 5) uncertainty in the knowledge of this tumble, and 6) the need to maneuver at least one of the satellites through an accelerated approach trajectory. This thesis considers challenges 3 through 6 by addressing the terminal approach and soft docking by a Chaser satellite to a passively tumbling, rigid-body Target. The terminal approach is characterized by the Chaser starting at an initial position several meters away from the Target and aligned with the Target's docking port. It then initializes its inward motion relative to the Target to maintain its position synchronous (i.e., maintaining alignment with the body-fixed frame of the Target's docking port) with the tumbling motion. Using a fuel-efficient trajectory, it traverses along the docking port's body-fixed approach axis by creating the requisite tangential and radial accelerations associated with the Target's tumble. Finally, the Chaser docks with a sufficiently low impact velocity to avoid damage to itself or the Target. This thesis addresses three important aspects of this Synchronous Docking to a Tumbling Target (SDTT) problem, with examples drawn from this ADR mission scenario. First, a methodology is developed to define whether a Chaser can feasibly execute this terminal approach to a Target when that Target's tumbling motion is measured a priori with some known degree of uncertainty. Given the potential urgency in deriving the approach trajectory, a robust and computationally efficient minimum fuel trajectory solver is formulated. This solver is based upon the recognition that fuel optimality requires that the tangential and radial accelerations of the Chaser be equal as it traverses the terminal approach. Since these accelerations are dictated by the Target's uncertain tumbling motion, a Multiple Model optimization technique is used to provide robustness in the trajectory. The result is a methodology that can assess the feasibility of achieving a soft dock of a known Chaser with a Target whose motion is uncertain. Second, this feasibility framework can be used to analyze two Chaser scenarios. The first entails the design of a new Chaser that can capture a broad sub-set of the Target population (Market Capture), while the second entails the determination of the fraction of a Target population, with uncertain dynamics, to which an existing Chaser can feasibly soft dock (Market Analysis). Both scenarios consider levels of uncertainty in the knowledge of the motion of individual Targets in the population that is inherently associated with remote sensing. Third, 0-g simulations are required to obtain predictions of Chaser performance, since this SDTT problem leads to Chasers that conduct multi-axis accelerations uncharacteristic of conventional satellites. A simulation framework that supports both unconstrained 0-g and constrained 1-g performance prediction to flight is developed. The development and validation of key dynamics and environmental factors for both environments are presented. As a result, this research provides a computationally efficient, low-order solver for rapidly deriving a terminal approach trajectory that is both fuel optimal as well as robust to uncertainty in the measurement of the Target's dynamics. Furthermore, a methodology is provided that permits evaluation of the design of a Chaser that can feasibly dock with a desired fraction of the Target population before committing to the cost and effort of developing that Chaser (Market Capture) as well as those Targets to which an existing Chaser can feasibly dock before committing to the time and fuel consumption needed to rendezvous with those Targets (Market Analysis). Finally, a ground test methodology for Chasers that must execute multi-axis accelerated trajectories is presented to minimize the impact of Chaser 0-g modeling errors on the performance of SDTT operations.
by David Charles Sternberg.
Sc. D.
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Amaee, Richard Dana. "Structural studies of PKS and NRPS docking domains." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613128.
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Strafford, J. "Docking and bioinformatics tools to guide enzyme engineering." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1339145/.
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The carbon-carbon bond forming ability of transketolase (TK), along with its broad substrate specificity, makes it very attractive as a biocatalyst in industrial organic synthesis. Through the production of saturation mutagenesis libraries focused on individual active site residues, several variants of TK have been discovered with enhanced activities on non-natural substrates. We have used computational and bioinformatics tools to increase our understanding of TK and to guide engineering of the enzyme for further improvements in activity. Computational automated docking is a powerful technique with the potential to identify transient structures along an enzyme reaction pathway that are difficult to obtain by experimental structure determination. We have used the AutoDock algorithm to dock a series of known ketol donor and aldehyde acceptor substrates into the active site of E. coli TK, both in the presence and the absence of reactive intermediates. Comparison of docked conformations with available crystal structure complexes allows us to propose a more complete mechanism at a level of detail not currently possible by experimental structure determination alone. Statistical coupling analysis (SCA) utilises evolutionary sequence data present within multiple sequence alignments to identify energetically coupled networks of residues within protein structures. Using this technique we have identified several coupled networks within the TK enzyme which we have targeted for mutagenesis in multiple mutant variant libraries. Screening of these libraries for increased activity on the non-natural substrate propionaldehyde (PA) has identified combinations of mutations that act synergistically on enzyme activity. Notably, a double variant has been discovered with a 20-fold improvement in kcat relative to wild type on the PA reaction, this is higher than any other TK variant discovered to date.
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Larkum, Trevor John. "Optimisation of docking locations for remotely operated vehicles." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1445650/.
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This thesis describes work aimed at developing practical methods for determining the best docking locations for an underwater remotely operated vehicle (ROV) when inspecting an offshore platform. ROVs are used extensively in the offshore oil and gas industry to conduct a large variety of intervention tasks such as visual inspection, operational monitoring, equipment installation and operation, debris recovery, and so on. However, they have found only limited use in the more difficult tasks such as the detailed inspection of complex weld geometries. These complex welds are, however, found extensively in the construction of the majority of offshore structures and platforms ('oil rigs'). Furthermore, there is a safety requirement to have them inspected regularly since failure of these welds can potentially lead to catastrophic failure of the structures, the majority of which are manned. A number of specialist ROV systems have been developed that are able to attach onto platform structures and use their manipulators to conduct inspection. However, due to the short reach of the manipulators and the complex geometry of the welds (often encumbered with protruding pipes and other fittings) the success of any inspection is crucially dependent on a good initial choice of ROV docking position. This thesis will describe the problems and current manual planning methods, and then detail the development of two new methods for automated optimisation of docking positions - firstly using neural networks, and secondly using more conventional numerical processing. This thesis will also review related work in the field, such as the development of neural networks and their applications in the general offshore environment and in the control of ROVs and robot manipulator arms, and other approaches to ROV docking. It will further describe the use of the system developed here for planning docking positions on example commercial ROV inspection work programmes.
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Rörbrink, Malin. "Improving detection of promising unrefined protein docking complexes." Thesis, Linköpings universitet, Bioinformatik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-133633.
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Understanding protein-protein interaction (PPI) is important in order to understand cellular processes. X-ray crystallography and mutagenesis, expensive methods both in time and resources, are the most reliable methods for detecting PPI. Computational approaches could, therefore, reduce resources and time spent on detecting PPIs. During this master thesis a method, cProQPred, was created for scoring how realistic coarse PPI models are. cProQPred use the machine learning method Random Forest trained on previously calculated features from the programs ProQDock and InterPred. By combining some of ProQDock’s features and the InterPred score from InterPred the cProQPred method generated a higher performance than both ProQDock and InterPred. This work also tried to predict the quality of the PPI model after refinement and the chance for a coarse PPI model to succeed at refinement. The result illustrated that the predicted quality of a coarse PPI model also was a relatively good prediction of the quality the coarse PPI model would get after refinement. Prediction of the chance for a coarse PPI model to succeed at refinement was, however, without success.
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Daunay, Bruno. "Couplage haptique pour des applications de docking moléculaire." Paris 6, 2007. http://www.theses.fr/2007PA066324.
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Réaliser une tâche de docking moléculaire avec un retour d'effort à six degrés de liberté suppose d'adresser trois difficultés majeures. Le fait de réutiliser un logiciel conçu pour des applications pharmaceutiques, suppose de s'adapter à celui-ci. La première difficulté consiste donc dans le temps de réponse du changement conformationnel de la protéine, qui n'est pas temps-réel. Les commandes risquent donc d'être instables. La différence d'échelle entre les efforts et les déplacements de l'environnement de l'utilisateur et de la molecule, ainsi que la forte raideur des forces intermoléculaires, posent un réel problème quant à l'interprétation des efforts. De plus, le simulateur moléculaire évalue une énergie d'interaction. Sa conversion en effort doit donc être envisagée. La plate-forme de téléopération mise en place, qui garantit un retour d'effort à six degrés de liberté, prend en compte ces difficultés, et propose : La réutilisation d'un logiciel de simulation moléculaire, intégrant un processus de minimisation de l'énergie calculée à partir d'un champ de force quelconque, interfacé avec un organe haptique de la classe Virtuose. Une commande en variables d'onde capable d'atténuer la grande amplitude des forces et de rendre passive la communication, retardée par le calcul du changement de conformation de la protéine. Des coefficients homothétiques font l'adéquation entre les grandeurs physiques des deux mondes. Une conversion de l'énergie d'interaction en effort à ressentir. Celle-ci est assurée par un modèle paramétrable utilisant la méthode des moindres carrés pour l'actualisation de ses paramètres. Sa dérivée analytique fournit les efforts d'interaction.
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Persson, Anton, and Rasmus Åslin. "Effektivisering av materialhantering på en cross-docking terminal." Thesis, Tekniska Högskolan, Jönköping University, JTH, Logistik och verksamhetsledning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:hj:diva-50014.
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Syfte – Rapportens syfte är att undersöka förbättringsmöjligheter av materialhantering mellan in-och utlastning på en cross-docking terminal. Baserat på syftet har två frågeställningar formulerats. Vilka aktiviteter ingår i materialhantering? Hur kan materialhanteringen effektiviseras? Metod – Studien har genomfört en förstudie på fallföretaget för att definiera ett problemområde. Utifrån problemområdet har syfte och frågeställningar formulerats. Fallstudien och litteraturgenomgång har genomförts parallellt för att skapa en abduktiv ansats. De inhämtade teorier från litteraturstudierna ligger stöd för det teoretiska ramverket. Resultat – Flera slöserier identifierades under studien vilket påverkar den interna materialhanteringen. Inom de primära cross-docking aktiviteterna existerar slöserier vilket behöver elimineras för en effektivisering ska genomföras. Studien lyfter även vikten av ett fungerande informationsflöde för en effektiv materialhantering. Implikationer – Eftersom problemområdet redan har etablerade teorier har ingen ny forskning genomförts. Däremot har studien inriktat sig på en annan synvinkel, där förhållandet mellan informationsflöde och materialflöde studerats. Begränsningar – Begreppet materialhantering är brett och innefattar även materialhantering utanför terminalen. Rapporten har begränsat sig till enbart den interna materialhanteringen. Studien begränsar sig till enbart ett fallföretag vilket påverkar generaliserbarheten. Nyckelord – Cross-docking, Materialhantering, Materialflöde, Informationsflöde.
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Tan, Wee Kiat. "Horizontal steering control in docking the ARIES AUV." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2003. http://library.nps.navy.mil/uhtbin/hyperion-image/03Dec%5FTan%5FW.pdf.
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Thesis (M.S. in Mechanical Engineering)--Naval Postgraduate School, December 2003.Thesis advisor(s): Fotis Papoulias, Anthony J. Healey. Includes bibliographical references (p. 83). Also available online.
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Miraglia, Italo Giorgio. "Applicazione della logica fuzzy al docking tra dirigibili." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amslaurea.unibo.it/6975/.
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Progetto e analisi delle performance di un controllore realizzato con la metodologia fuzzy per una manovra di docking fra due dirigibili. Propedeutica a questo, è stata la campagna, presso la galleria del vento messa a disposizione dalla Clarkson University, di raccolta di dati sperimentali, che sono stati poi utilizzati per realizzare un simulatore con cui testare il controllore.
Nel primo capitolo, si è presentato la tecnologia dei dirigibili, le varie tipologie ed una descrizione dei moderni concepts. Successivamente, sono state presentate le applicazioni nelle quali i moderni dirigibili possono essere impiegati. L’ultima parte tratta di due esempi di docking fra mezzi aerei: il rifornimento in volo e i “parasite aircrafts”.
Il secondo capitolo, tratta della logica utilizzata dal controllore: la logica fuzzy. Le basi della teoria insiemistica classica sono state il punto di partenza per mostrare come, introducendo le funzioni di appartenenza, sia possibile commutare tra la teoria classica e fuzzy. La seconda parte del capitolo affronta le nozioni della teoria fuzzy, esponendo la metodologia con la quale è possibile inserire un controllore di questo tipo in un sistema “tradizionale”.
Il terzo capitolo presenta il modello di volo dei dirigibili. Partendo dalla legge di Newton, introdotto il concetto di inerzia e massa aggiunte, si arriva alle equazioni del moto non lineari. L’ultima parte è stata dedicata alla linearizzazione delle equazioni e alla condizione di trim.
Il quarto capitolo riguarda la campagna sperimentale di test in galleria del vento, con la realizzazione dei modelli in scala e la calibrazione della bilancia; successivamente, nel capitolo si commentano i dati sperimentali raccolti.
Il quinto capitolo, mostra la metodologia con cui è possibile progettare un controllore fuzzy per il controllo della manovra di docking fra dirigibili. La seconda parte mostra le performance ottenute con questo tipo di sistema.
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Gaultier, Mathieu. "An Autonomous Self-Docking Robot on Passive Systems." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-272122.
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The design of a robot is tightly linked to it assigned task. A robot does not have the same adaptability as humans do. Therefore every robot is designed to achieve one specific task. An increasing alternative to this issue are modular robots. Since one can not achieve the task alone, it requires the help of others. In this thesis is studied the possibility of having one single ground robot managing the displacement task instead of implementing sensors and algorithms on each independent autonomous systems. The displacement robot should have the ability to plug itself to some others so that it can then drive them around at their desired places. This thesis work is especially focusing on this docking sequence between the displacement robot and the other module. The achievement of this docking sequence relies on the use of fiducial markers to extract the relative poses of the two systems. Furthermore, the noisiness of the obtained measure has been dealt with Extended Kalman Filters and Monte Carlo Localisation algorithms. The results obtained through the simulations shown that a MCL algorithm would provide better results for such systems. However the output relative poses were not precise enough for the system to actually plug connectors and ensure the communication between the two systems.Utformningen av en robot är nära kopplad till dess tilldelade uppgift. En robot har inte samma anpassningsförmåga som människor. Därför är varje robot utformad för att lösa en specifik uppgift. Ett alternativ till detta är modulära robotar, vilket ökar i populäritet. En robot kräver andras hjälp eftersom den inte kan klara uppgiften ensam. I detta examensarbete undersöks möjligheten att ha en enda markrobot som hanterar förflyttningsuppgiften istället för att implementera sensorer och algoritmer på varje oberoende system. Förflyttningsroboten bör ha förmågan att ansluta sig till vissa andra moduler så att den sedan kan styra dem på önskade platser. Detta examensarbete fokuserar särskilt på dockningssekvensen mellan förflyttningsroboten och den andra modulen. För att uppnå denna dockningssekvens används visuella markörer för att extrahera de relativa positionerna för de två systemen. Dessutom har Kalmanfilter och Monte Carlo-lokaliseringsalgoritmer undersökts. Resultaten som erhållits genom simuleringarna är korrekta men de beräknade relativa positionerna var inte tillräckligt exakta för att systemen faktiskt skulle kunna ansluta och säkerställa kommunikationen mellan dem.
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Landaverde, Raphael J. "GPU optimizations for a production molecular docking code." Thesis, Boston University, 2014. https://hdl.handle.net/2144/21199.
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Thesis (M.Sc.Eng.) -- Boston UniversityScientists have always felt the desire to perform computationally intensive tasks that surpass the capabilities of conventional single core computers. As a result of this trend, Graphics Processing Units (GPUs) have come to be increasingly used for general computation in scientific research. This field of GPU acceleration is now a vast and mature discipline. Molecular docking, the modeling of the interactions between two molecules, is a particularly computationally intensive task that has been the subject of research for many years. It is a critical simulation tool used for the screening of protein compounds for drug design and in research of the nature of life itself. The PIPER molecular docking program was previously accelerated using GPUs, achieving a notable speedup over conventional single core implementation. Since its original release the development of the CPU based PIPER has not ceased, and it is now a mature and fast parallel code. The GPU version, however, still contains many potential points for optimization. In the current work, we present a new version of GPU PIPER that attains a 3.3x speedup over a parallel MPI version of PIPER running on an 8 core machine and using the optimized Intel Math Kernel Library. We achieve this speedup by optimizing existing kernels for modern GPU architectures and migrating critical code segments to the GPU. In particular, we both improve the runtime of the filtering and scoring stages by more than an order of magnitude, and move all molecular data permanently to the GPU to improve data locality. This new speedup is obtained while retaining a computational accuracy virtually identical to the CPU based version. We also demonstrate that, due to the algorithmic dependencies of the PIPER algorithm on the 3D Fast Fourier Transform, our GPU PIPER will likely remain proportionally faster than equivalent CPU based implementations, and with little room for further optimizations. This new GPU accelerated version of PIPER is integrated as part of the ClusPro molecular docking and analysis server at Boston University. ClusPro has over 4000 registered users and more than 50000 jobs run over the past 4 years.
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EKSTRÖM, ELIN, and ELLEN SEVERINSSON. "A Conceptual Design of a Reliable Hard Docking System : Docking of an utonomous underwater vehicle to the new generation A26 submarine." Thesis, KTH, Skolan för industriell teknik och management (ITM), 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-299330.
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In year 2024 and 2025 the Royal Swedish Navy is expected to launch two new submarines with new possibilities to dock underwater vehicles. The submarines are part of the new Blekinge Class (A26) and will aid the Swedish Armed Forces and the Swedish Defense Materiel Administration (FMV) in their aim to develop and use more autonomous systems, to increase staff efficiency and to face the technological challenges of tomorrow. This thesis was carried out at FMV, with the purpose of investigating the physical requirements put on the new submarines, when docking an autonomous underwater vehicle. These requirements were identified through an analysis of qualitative and quantitative research. The analysis resulted in ten key insights, which led to thirteen requirements. The requirements were combined with project specific data of the AUV62 system and A26 submarine, to develop three conceptual designs of hard docking systems. The concepts were verified through analysis of material, stress and deflection, and geometric constraints. The concepts were evaluated based on how well they were fulfilling each requirement. A hammock-alike concept was shown to have most potential in being the most reliable hard docking system. The thesis ended with concluding that its purpose had been fulfilled, followed with recommendations for continued work.Under 2024 och 2025 förväntas Svenska Marinen sjösätta två nya ubåtar, med nya förmågor gällande dockning av undervattensfordon. Ubåtarna ingår i nya Blekingeklass (A26) och är en del av Försvarsmaktens och Försvarets Materielverks (FMV) målsättning om att utveckla och använda mer autonoma system, för att öka personaleffektivitet och för att kunna möta morgondagens tekniska utmaningar. Detta examensarbete utfördes på uppdrag av FMV, med syftet att undersöka vilka fysiska krav som ställs för att hårddocka ett autonomt undervattensfordon på de nya ubåtarna. Dessa krav identifierades genom analys av en kvalitativ och kvantitativ undersökning. Analysen uppdagade tio nyckelinsikter som gav upphov till tretton krav. Kraven kombinerades med projektspecifik data för AUV62-systemet och ubåt A26, för att utveckla tre konceptuella designförslag av hårddockningssystem. Koncepten verifierades genom analys gällande material, spänning och utböjning, samt geometriska begränsningar. Koncepten utvärderades baserat på hur väl de uppfyllde respektive krav. Ett hängmatteformat koncept visade sig ha störst potential för att bli ett pålitligt hårddockningssystem. Examensarbetet avslutades med att projektets syfte ansågs vara uppfyllt, följt av förslag på vidare arbete.
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Grimm, Vera. "Untersuchung eines wissensbasierten Potentials zur Bewertung von Protein-Protein-Docking-Studien." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=967176506.
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Zimmermann, Olav. "Untersuchungen zur Vorhersage der nativen Orientierung von Protein-Komplexen mit Fourier-Korrelationsmethoden." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=96830933X.
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Koch, Kerstin. "Statistical analysis of amino acid side chain flexibility for 1:n protein protein docking." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968919413.
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Magalhães, Camila Silva de. "Algoritmos genéticos para o problema de Docking proteína-ligante." Laboratório Nacional de Computação Científica, 2006. http://www.lncc.br/tdmc/tde_busca/arquivo.php?codArquivo=85.
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Métodos de docking receptor-ligante são métodos computacionais para a identificação do modo de ligação de moléculas candidatas a fármacos, no sítio ativo de proteínas consideradas como alvos moleculares para o tratamento quimioterápico de doenças. Estes métodos são uma parte importante no Desenho Racional de Fármacos Baseado em Estruturas e possuem grande potencial para auxiliar na descoberta de novos medicamentos.
Entretanto, a necessidade da inclusão dos graus de liberdade conformacionais relacionados à flexibilidade molecular, torna o problema de docking complexo e difícil de se resolver computacionalmente.
Por outro lado, algoritmos genéticos são métodos computacionais estocásticos inspirados na teoria da evolução de Darwin, que têm sido aplicados com sucesso à uma grande variedade de problemas complexos em ciência e engenharia.
O desenvolvimento de métodos de docking mais eficientes e com maior capacidade de predição constitui atualmente uma área de pesquisa altamente ativa.
Neste trabalho, foram implementadas e analisadas várias estratégias em algoritmos genéticos (AG's) para o problema de docking receptor-ligante.
Uma nova técnica para a preservação de múltiplas soluções foi desenvolvida. O método proposto é baseado na técnica de Seleção por Torneio Restrito (RTS) e tem como objetivo favorecer a preservação dos "nichos" e soluções de melhor qualidade na população.
Os métodos implementados foram testados em estudos de "re-docking" e "cross-docking" de inibidores da enzima HIV-1 protease com alto grau de flexibilidade conformacional. Os resultados obtidos mostram que a utilização de técnicas de múltiplas soluções que permitem a preservação de diversidade "útil" podem ser uma ferramenta poderosa no "docking" de ligantes altamente flexíveis, geralmente associados à hipersuperfícies de energia complexas. Estas estratégias aumentam a probabilidade de se encontrar soluções próximas das estruturas determinadas experimentalmente, além de permitir a determinação e posterior investigação de distintos modos de ligação ligante-receptor.
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Saladin, Adrien [Verfasser]. "Macromolecular Docking. Applications to the RecA nucleofilament / Adrien Saladin." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2010. http://d-nb.info/1034989146/34.
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Mylonas, George P. "Gaze-Contingent Perceptual Docking for Minimally Invasive Robotic Surgery." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.511834.
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De, Youngster Dela. "An Isometry-Invariant Spectral Approach for Macro-Molecular Docking." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30226.
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Proteins and the formation of large protein complexes are essential parts of living organisms. Proteins are present in all aspects of life processes, performing a multitude of various functions ranging from being structural components of cells, to facilitating the passage of certain molecules between various regions of cells. The 'protein docking problem' refers to the computational method of predicting the appropriate matching pair of a protein (receptor) with respect to another protein (ligand), when attempting to bind to one another to form a stable complex.
Research shows that matching the three-dimensional (3D) geometric structures of candidate proteins plays a key role in determining a so-called docking pair, which is one of the key aspects of the Computer Aided Drug Design process. However, the active sites which are responsible for binding do not always present a rigid-body shape matching problem. Rather, they may undergo sufficient deformation when docking occurs, which complicates the problem of finding a match.
To address this issue, we present an isometry-invariant and topologically robust partial shape matching method for finding complementary protein binding sites, which we call the ProtoDock algorithm. The ProtoDock algorithm comes in two variations. The first version performs a partial shape complementarity matching by initially segmenting the underlying protein object mesh into smaller portions using a spectral mesh segmentation approach. The Heat Kernel Signature (HKS), the underlying basis of our shape descriptor, is subsequently computed for the obtained segments. A final descriptor vector is constructed from the Heat Kernel Signatures and used as the basis for the segment matching. The three different descriptor methods employed are, the accepted Bag of Features (BoF) technique, and our two novel approaches, Closest Medoid Set (CMS) and Medoid Set Average (MSA).
The second variation of our ProtoDock algorithm aims to perform the partial matching by utilizing the pointwise HKS descriptors. The use of the pointwise HKS is mainly motivated by the suggestion that, at adequate times, the Heat Kernel Signature of a point on a surface sufficiently describes its neighbourhood. Hence, the HKS of a point may serve as the representative descriptor of its given region of which it forms a part. We propose three (3) sampling methods---Uniform, Random, and Segment-based Random sampling---for selecting these points for the partial matching. Random and Segment-based Random sampling both prove superior to the Uniform sampling method.
Our experimental results, run against the Protein-Protein Benchmark 4.0, demonstrate the viability of our approach, in that, it successfully returns known binding segments for known pairing proteins. Furthermore, our ProtoDock-1 algorithm still still yields good results for low resolution protein meshes. This results in even faster processing and matching times with sufficiently reduced computational requirements when obtaining the HKS.
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Keller, Kevin Martin. "Sonar based positioning and docking for autonomous underwater vehicles." Thesis, University of Liverpool, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399134.
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Livoti, Elsa Livoti. "Experimentally validated computational docking to characterize protein-protein interactions." Thesis, University of Kent, 2017. https://kar.kent.ac.uk/67450/.
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Each biomolecule in a living organism needs to adopt a specific threedimensional conformation to function properly. Function itself is usually achieved by specific interactions between biomolecular units. Structural knowledge at atomic level of biomolecules and their interaction is important to understand the mechanisms leading to biological response and to develop strategies to interfere with them when necessary. Antibodies are molecules of the immune system playing an ever more prominent role in basic research as well as in the biotechnology and pharmaceutical sectors. Characterizing their region of interaction with other proteins (epitopes) is useful for purposes ranging from molecular biology research to vaccine design. During my PhD studies I used a combination of solution NMR mapping, molecular biology and computational docking to provide a structural and biophysical characterization of new neutralizing antibodies from Dengue virus recovered subjects, comparing the binding of the same antibody to the four Dengue serotypes and the binding of different antibodies to the same serotype. We were able to rationally mutate an antibody to first alter its selectivity for different viral strains and then increase its neutralization by ~40 folds. For the first time, this was achieved without the availability of an x-ray structure. In a second sub-project, I investigated the interaction of the chemokine CXCL12 with the chromatin-associated protein HMGB1, confirming their direct interaction (only proposed but never proved before) and providing a structural explanation for the HMGB1 dependent increase of CXCL12 cellular activity. High profile publications resulted from the two above projects. The above mentioned projects relied heavily on solution NMR spectroscopy, which is ideally suited to the atomic level characterization of intermolecular interfaces and, as a consequence, to antibody epitope discovery. Having provided a residue-level description of a protein-protein interface by NMR, we subsequently used this experimental information to guide and validate computational docking experiments aimed at providing a three dimensional structure of the protein-protein (or antibody-protein) complex of interest. In collaboration with other members of my research group I validated the use of NMR and computational simulations to study antibody-antigen interactions, publishing two reviews in collaboration with other members of my research group.