Academic literature on the topic 'Docking energy definition'

The group of authors has carried out a number of works on a virtual simulation of a promising airtransport system (ATS) of balloon type within the MAAT project (Multibody Advanced Airship for Transport) jointly with Free University of Brussel (Vrije Universiteit Brussel, VUB). For the virtual simulation there was used Solid Works system. At modeling we were guided by the principles of a maximum detailed elaboration and interactive estimation. The fulfillment of a form analysis with the purpose of the definition of volume influence upon functional ATS possibilities, optimum use of aerodynamics and photogalvanic energy and also structure mass reduction became the result of this. Further there were carried out strength computations of structural elements of a carriage module, the estimation of safety margin for the virtual simulation of a docking process and docking unit functioning. To carry out an engineering analysis through the method of finite elements there was carried out a virtual simulation of the ATS in the FEMAP system. On a basis of the strength computation there were revealed the weakest sides of a structure and corrected before its creation. Autodesk 3ds Max was used for the creation of a virtual model with the purpose of design development. At the development of designproject the principles of virtual simulation were used. Kandinsky’s theory was used for the color choice of ATS MAAT models. As a result there were developed 3D models and made designmodels of a basic module, carriage module and a docking unit of a transport system with the use of techniques for a quick prototyping and 3D print. There were carried out strength computations of structural elements of a basic module, carriage module, a docking unit with the estimation of safety margin.

Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-derived donor and acceptor substrates and hetero-transglycosylation reactions with a variety of structurally diverse polysaccharides. In this work, we describe the basis of acceptor substrate binding specificity in non-specific Tropaeolum majus (TmXET6.3) and specific Populus tremula x tremuloides (PttXET16A) XETs, using molecular docking and molecular dynamics (MD) simulations combined with binding free energy calculations. The data indicate that the enzyme-donor (xyloglucan heptaoligosaccharide or XG-OS7)/acceptor complexes with the linear acceptors, where a backbone consisted of glucose (Glc) moieties linked via (1,4)- or (1,3)-β-glycosidic linkages, were bound stably in the active sites of TmXET6.3 and PttXET16A. Conversely, the acceptors with the (1,6)-β-linked Glc moieties were bound stably in TmXET6.3 but not in PttXET16A. When in the (1,4)-β-linked Glc containing acceptors, the saccharide moieties were replaced with mannose or xylose, they bound stably in TmXET6.3 but lacked stability in PttXET16A. MD simulations of the XET-donor/acceptor complexes with acceptors derived from (1,4;1,3)-β-glucans highlighted the importance of (1,3)-β-glycosidic linkages and side chain positions in the acceptor substrates. Our findings explain the differences in acceptor binding specificity between non-specific and specific XETs and associate theoretical to experimental data.

Background: Electrostatic interactions are one of the forces guiding the binding of molecules to proteins. The assessment of this interaction through computational approaches makes it possible to evaluate the energy of protein-drug complexes. Objective: Our purpose here is to review some the of methods used to calculate the electrostatic energy of protein-drug complexes and explore the capacity of these approaches for the generation of new computational tools for drug discovery using the abstraction of scoring function space. Method: Here we present an overview of AutoDock4 semi-empirical scoring function used to calculate binding affinity for protein-drug complexes. We focus our attention on electrostatic interactions and how to explore recently published results to increase the predictive performance of the computational models to estimate the energetics of protein-drug interactions. Public data available at Binding MOAD, BindingDB, and PDBbind were used to review the predictive performance of different approaches to predict binding affinity. Results: A comprehensive outline of the scoring function used to evaluate potential energy available in docking programs is presented. Recent developments of computational models to predict protein-drug energetics were able to create targeted-scoring functions to predict binding to these proteins. These targeted models outperform classical scoring functions and highlight the importance of electrostatic interactions in the definition of the binding. Conclusion: Here, we reviewed the development of scoring functions to predict binding affinity through the application of a semi-empirical free energy scoring function. Our studies show the superior predictive performance of machine learning models when compared with classical scoring functions and the importance of electrostatic interactions for binding affinity.

Within the objectives of the H2020 DIAMOND project, the paper investigates women’s needs and expectations as users of the bike-sharing service managed by Syndicat Mixte Autolib et Velib Métropole in the territory of Paris Region-Petite Couronne (France). The paper presents a thematic literature review focused on gender inclusion in bike-sharing schemes. The proposed methodological approach is based on (i) Geographic Information Systems for the analysis of geolocated open datasets related to land, sociodemographic and mobility characteristics of the areas surrounding each docking stations. This was aimed at identifying a short list of suitable bike-sharing docking stations, which were further characterized through: (ii) structured proprietary data focused on travel demand; (iii) onsite observations focused on universal design indicators; (iv) survey questionnaires focused on women’s concerns, needs and expectations; and (v) social media data from Twitter focused on the opinion of the end-users. Results showed that women use the VELIB’s bike-sharing service much less than men (about 30% of the total number of users), since they are more concerned about the following issues: accessibility (e.g., availability of bikes at the docking stations, distance to the nearest station, type and quality of the cycle paths); safety and security (e.g., perception of danger and insecurity while cycling and using the current bicycle infrastructures); social constraints (e.g., perceptions and cultural stigmatization associated with cycling and bike-sharing); weather and topography (e.g., impact of weather and the urban terrain on cycling and bike-sharing). The final aim of the H2020 DIAMOND project is to support the definition of guidelines and policies for the inclusion of women’s needs in the design of future bike-sharing services.

BackgroundPain is an unpleasant sensory and emotional experience that causes human suffering.1 Its prevalence has increased, as well as the abuse and dependence on strong opioids.2,3 The α-phellandrene is a terpene that exerts antinociceptive and immunostimulant effects,4 however, its mechanisms remain to be elucidated. In this way, bioinformatics may assist in developing new therapeutic approaches for pain management.ObjectivesTo investigate the action of a-PHEL in chronic pain, focusing on the role of the serotoninergic system, to develop a new therapeutic tool without the side effects of conventional drugs.MethodsMolecular docking is an important method for the investigation of the mechanism of action of natural compounds. It is possible to evaluate the molecular dynamics, elucidating the stability of complexes. The software PyMOL and AutoDock Vina 1.5.7 were used to predict interactions of a-PHEL and 5-HT2AR.The mechanism of action of a-PHEL in chronic pain was analyzed in vivo as well. The Ethics Committee of UFPI approved this project (protocol n° 305/17). Female Swiss mice (25-30 g) underwent partial sciatic nerve ligation surgery to induce neuropathy. The neuropathic mice (N=6) were pre-treated with 5-HT2A receptor antagonist Ketanserin (0,3 mg/kg, i.p.) or Saline (10 mL/kg, p.o.). After 20min, they were treated with α-phel (6,25 mg/kg, p.o.) and after 1h they were evaluated by the Von Frey test.ResultsThe serotoninergic system has a complex and important role in pain modulation especially through descending inhibitory pathways. The Molecular docking predicted the positioning of a-PHEL in the 5-HT2AR, aiding the understanding of its biological activity. The analysis identified 9 key positions for the ligand binding in 5-HT2AR. The lowest Gibbs free energy ΔG= -6.9 kcal/mol. The negative binding energy indicates a strong and stable bond, therefore, α-PHEL has a high affinity for the receptor (Figure 1).Figure 1.Graphical 3D representation of the binding mode of α-PHEL with 5-HT2AR. A - The ligand (orange) is shown surrounded by a molecular surface of the receptor (green). B – Representation of the best-scoring docked pose (-6.9 kcal/mol) of a-PHEL (orange).Excellent in vivo therapeutic effects were observed in the animal model of neuropathic pain. Regarding the pharmacological in vivo analysis, the a-PHEL significantly decreased the pain threshold (P<0.05), exhibiting an anti-hypersensitive effect. The inhibition of serotonergic transmission by pretreatment with Ketanserin significantly reduced the antinociceptive effect of a-PHEL in mice.The data indicate that a-PHEL exerts its antinociceptive effect on chronic neuropathic pain model by activation of the 5-HT2AR receptor. Its analgesic effect seems to be mediated by descending inhibitory serotonin system interfering with pain impulse transduction.ConclusionChronic pain is often resistant to medical treatment and the cheminformatics techniques may facilitate the discovery of new compounds, guiding towards specific molecular targets.The a-PHEL may act as a serotoninergic agonist, reducing mechanical sensitivity. It is a promising compound for chronic pain treatment, with lower cost and fewer adverse effects than opioids. Future investigations are expected to highlight the in-depth effects of the interaction of a-PHEL with other receptor subtypes.References[1]Raja SN, et al. The revised International Association for the Study of Pain definition of pain: concepts, challenges, and compromises. Pain. 2020;161(9):1976-1982.[2]Xie J, et al. Temporal trends of opioid use among incident osteoarthritis patients in Catalonia, 2007-2016: a population-based cohort study. Annals of The Rheumatic Disease. 2020; 79 (sl. 1): 174.[3]Liktor-Busa E, et al. Analgesic Potential of Terpenes Derived from Cannabis sativa. Pharmac Rev. 2021, 73(4):98-126.[4]Pinheiro FR, et al. α-Phellandrene exhibits antinociceptive and tumor-reducing effects in a mouse model of oncologic pain. Tox Appl Pharmacol. 418(1), 2021Disclosure of InterestsNone declared.

Chronic fatigue syndrome (CFS), also known as myalgic encephalomyelitis (ME) or systemic exertional intolerance disease (SEID), is an illness dominated by long-term fatigue persisting for more than six months, incapacitating to the point of sufferers being bedridden or housebound in some cases, and unexplained by some other underlying medical condition. CFS is also often characterised by unrefreshing sleep, post-exertional discomfort ranging from malaise to extreme exhaustion, orthostatic (upright posture) intolerance, muscle pain, cognitive impairment (including the commonly described symptom of "brain fog"), and deterioration in cellular bioenergetics [1-3]. Scientific estimates of the world-wide population percentage that suffer from CFS naturally vary, but a conservative estimate based on several studies is at least 0.4%, thereby equating to millions world-wide [1-4]. Thankfully, after decades of dismissal by some quarters, leading to despair and exasperation of sufferers, CFS is now widely accepted as a legitimate illness. However, while depreciating labels such as "yuppy flu" have subsequently been banished to recent history, this new-found acceptance provides comfort for sufferers only up to a certain point. Viz., CFS is still far from fully understood and is often described as a complex, multisystem illness with no clear pathological mechanisms or diagnostic biomarkers [1-3], from which treatment uncertainty ensues [1,2]. Sadly, due in no small part to this uncertainty and the illness characteristics of the opening paragraph, the suicide rate of CFS sufferers has been reported as approximately seven times that of their healthy counterparts [1,5]. The economic and other social impacts of CFS are difficult to determine because of the arbitrariness of case definitions, lack of evidence including prevalence data, diagnostic inability of some physicians due to factors such as disbelief and lack of understanding (one major survey [4] reveals that 62% of sufferers are not confident in their general physician’s understanding), and difficulty many sufferers have in explaining the symptoms of their illness (another survey [2] shows that a majority or substantial proportion, depending on factors such as country of origin, have difficulty explaining their illness to not only physicians but also family and friends). Societal impacts of CFS have nonetheless been assessed by various committees (e.g., associated with the United States’ Institute of Medicine) and working/action groups (e.g., associated with the European Union). As expected, the economic impact of CFS is formally declared to be significant, with the net income of a CFS household in Europe being substantially lower than general population households (i.e., individual productivity effect), and the total annual cost burden being tens of billions of dollars in the United States alone [1-4]. The World Health Organization generally classifies CFS as a neurological illness involving the central nervous system. Some notable and more specific examples of proposed CFS aetiology components are summarised below, with these examples reflecting the complex multisystem nature of CFS and not necessarily being mutually exclusive: • Recent studies suggest that CFS arises from functional changes in the brain, with spectroscopic and inflammatory brain changes (e.g., following repeated exercise) also demonstrated. However, uncertainty over the character, location and propensity of such changes remains and the need for further functional neuroimaging studies is recognised [2,3,6,7]. • A significant increase in red blood cell (RBC) stiffness is reported in CFS, suggesting that compromised RBC transport through microcapillaries may contribute to CFS aetiology and that this diminished deformability could form the basis of a first-pass diagnostic test [8]. Further to this point, the previously identified CFS characteristic of orthostatic intolerance (estimated to occur in up to 97% of cases) is linked to under-oxygenatation of the brain to which diminished RBC deformability is thought to be a contributing factor [9]. • Unusual RBC shape, leading to reduced blood flow and changes in molecular docking on the RBC surface, is reported in CFS [10]. The subsequent increase in the number of stomatocytes (RBCs that have lost their typical concave shape, due for example to membrane defect), adds to the previous point of diminished RBC deformability to support poor microcirculation as contributing to CFS aetiology. • Dysfunction of mitochondria (subcellular organelles within the cytoplasm of aerobic cells) is found in CFS, with the interference of adenosine triphosphate (ATP) production being one of several consequences within the explanatory pathological pathway [11] (ATP is fundamentally essential for cellular-level metabolic energy requirements as outlined in Section 3). • CFS is largely resolved as not being attributable to some ongoing infection, endocrine disorder, or psychiatric condition [3,6]. While some similarly do not assign an immunological disorder attribution, more often over-stimulation or over-reaction of the immune system (hyperimmune response), impaired immune system response, immuno-inflammatory, and oxidative damage to the immune system, are all utilised expressions associated with CFS [3,6,8,1113], which in several research circles is described as a neuroimmune disease [1,11,14]. This immunological quandary again highlights the complexity of the ongoing medical challenge at hand. One clear aspect of CFS is that underlying pathophysiology implicates a range of different acute infections as onset triggers in a significant minority of cases (i.e., infections like Epstein-Barr, Ross River and the 2003 outbreak variant of Severe Acute Respiratory Syndrome, or SARS, viruses). No other medical or psychological factors are definitively implicated in CFS [7]. For many observers such triggerings are mindful of, if not directly related to, the crippling fatigue that is widely reported within contemporary media and recent studies as a lasting symptom of COVID-19. Such COVID-19-triggred CFS has led to the coined phrases of COVID-19 "long-haulers" or "long COVID", and has returned CFS to the public awareness spotlight [12]. However, too familiarly the lack of definitive CFS biomarkers is again confirmed by long COVID research, and sadly the dismissive attitudes of some in the medical profession is also a point of exasperation for long COVID sufferers [12], contributing for example to the in-desperation-establishment of a "long COVID kids" Facebook site in the United Kingdom. Established treatments, such as cognitive behaviour therapy (CBT) and graded exercise therapy (GET), primarily aim to manage the symptoms and improve the overall function of sufferers. The confounding nature of CFS extends to these treatments, since there is wide ongoing debate over their effectiveness [1,15]. For example, while GET is shown to benefit some, for others it is essentially considered just "cruel". A host of alternative treatments, some of which may be described as holistic or naturopathic or similar, naturally also exist, such as cryogenic, floatation and oxygen therapies, to name just a few. It is not the intention or place of the present article to compare, critique or scientifically review such treatments. It will simply be stated that, at least anecdotally, some such treatments seem to bring relief to some individuals (which is a positive outcome for those lucky enough to find any relief), but certainly most do not consider these treatments to be CFS cures or long-term major alleviators for the majority. Contemporary scientific scrutiny into how COVID-19 can damage the brain [13,16,17], and suggesting that the virus’ fatigue and adverse neurological effects (such as loss of smell and taste, altered mental states that can lead to the development of psychoses, and brain shrinkage in regions essential for processing memory, cognition and emotion) are indeed due to some hyperimmune response with neuroinflammation, does however offer many CFS sufferers new hope. Viz., hope that as a result of such scrutiny highly effective treatments (e.g., neural rewiring therapies [16]) and eventual cure await, even with the caveat of caution around some uncertain degree of overlap between COVID and non-COVID CFS. The present article’s title with cartoon of a fatigued physicist upon first glance likely appears incongruous. However, while some delight was taken in choosing this "humorous-to-a-physicist" title, the article is journalistically serious and does not make light of CFS. Rather, in addition to the above CFS overview, the article reflects upon a presented clinical Case Study of a seemingly recovering CFS sufferer, to form a justified CFS hypothesis for future testing. The to-be-formed hypothesis follows from the unique neuro-perspectives of [18], which explore central nervous system impulse encoding revelations via a new approach to high-order electroencephalogram (EEG) phase analysis. Given that CFS has a neurological component, can these new perspectives be applied to the area of CFS, and in particular to the to-be-presented Case Study of recovery? While this tangent might seem a long bow to draw, perhaps a fresh CFS perspective is just what is currently needed. Despite the quantum mechanical aspects to come and references [18] and [19], the latter on a discrete oscillator phase noise effect applied within phase-shift keying radiofrequency (RF) digital signal modulation, being recommended prior readings for those with a biomedical engineering or similar background, no such specialist backgrounds are assumed for readers. In brief, the present article represents academic (science and medicine) journalism that is hopefully considered high-interest, and shares via Case Study the clinical/medical results, collated over several years, for a scientifically dependent individual. The eventually formed hypothesis is intended for testing within a future formalised study, and so presently may be countered by alternative explanatory hypotheses, such as placebo and simple recovery coincidence, which are also identified.

Cancer stem cells (CSCs) are subpopulation of cells which have been demonstrated in a variety of cancer models and involved in cancer initiation, progression, and development. Indeed, CSCs which seem to form a small percentage of tumor cells, display resembling characteristics to natural stem cells such as self-renewal, survival, differentiation, proliferation, and quiescence. Moreover, they have some characteristics that eventually can demonstrate the heterogeneity of cancer cells and tumor progression. On the other hand, another aspect of CSCs that has been recognized as a central concern facing cancer patients is resistance to mainstays of cancer treatment such as chemotherapy and radiation. Owing to these details and the stated stemness capabilities, these immature progenitors of cancerous cells can constantly persist after different therapies and cause tumor regrowth or metastasis. Further, in both normal development and malignancy, cellular metabolism and stemness are intricately linked and CSCs dominant metabolic phenotype changes across tumor entities, patients, and tumor subclones. Hence, CSCs can be determined as one of the factors that correlate to the failure of common therapeutic approaches in cancer treatment. In this context, researchers are searching out new alternative or complementary therapies such as targeted methods to fight against cancer. Molecular docking is one of the computational modeling methods that has a new promise in cancer cell targeting through drug designing and discovering programs. In a simple definition, molecular docking methods are used to determine the metabolic interaction between two molecules and find the best orientation of a ligand to its molecular target with minimal free energy in the formation of a stable complex. As a comprehensive approach, this computational drug design method can be thought more cost-effective and time-saving compare to other conventional methods in cancer treatment. In addition, increasing productivity and quality in pharmaceutical research can be another advantage of this molecular modeling method. Therefore, in recent years, it can be concluded that molecular docking can be considered as one of the novel strategies at the forefront of the cancer battle via targeting cancer stem cell metabolic processes.

Virtual High Throughput Screening (vHTS) has an increasingly important role in lowering both costs and time in drug discovery. The present work deals with the development (C++ programming language) of a new molecular docking software (semi-flexible model) to be used for vHTS. It would improve some of the main aspects of this type of softwares in current use, with particular reference to the program AutoDock: a particular importance is given to the calculation of the ligand conformational energy variation in passing from the unbound to the bound state, which represents a crucial term in the docking energy definition. Two real cases to which the new software modules were applied are then presented: the first belonging to drug discovery, concerning the study of new Ras oncogenic protein inhibitors; the second belonging to virtual protein engineering (VPE), concerning the design of a modified enzyme to be used in the manufacturing of semisynthetic antibiotics.

With deepening ocean development , a larger scale Internet of Underwater Things (IoUT) is being realized[1].More and more underwater equipment is being deployed, various ocean monitoring equipment, underwater robots and underwater group sites amongst others, all of which will be working in the deep sea for long periods of time in the foreseeable future[2].Due to the increasing working time and power consumption, it has become difficult for the high energy batteries carried by these facilities to cover their energy needs [3]. Therefore, it is necessary to solve the problem of electrical energy replenishment for underwater equipment.Based on Equinor’s Underwater Intervention Drone (UID) standard interface definition, Blue Logic have produced the world's first three universal, open-standard subsea drone docking stations.But this is not perfect, in the face of deeper waters, more complex multi-shape deep sea equipment charging needs, the current program is not enough to solve[4].Therefore, based on the IoUT scenario positioning, this research designs a subsea charging station that can serve multiple devices.The concept is similar to a land-based collection station for power banks, providing multiple sub-charging equipment that can be carried on the move to charge multiple subsea equipments of different types simultaneously.It also uses ocean energy to provide in-situ produced electricity for the underwater charging base station .Compared to Blue Logic's Subsea Drone Docking Station (SDS), it enables the multi-device charging needs of the IoUT using ultrasonic technology[5,6].In the long term, the combination of existing equipment will greatly reduce the cost of regional subsea long-term exploration and expand the scope of exploration[7].The paper will solve the following problems:1) How to solve the charging problem of long-distance survey of underwater equipments（e.g. AUV）?2) How to make the design applicable to charging usage scenarios common to different types, forms and sizes of underwater equipments?3) How to design underwater charging energy transmission more efficiently and sustainably?The research approach composed following parts:- Through literature research, sort out the development status of technical equipment such as underwater charging, underwater docking, underwater information transmission and marine power generation.- A structure interview with the opinions of deep-sea equipment designers and researchers to clarify the design requirements. - Analyze product features and problems and summarize the design process and direction through brainstorming method and solution building method.The design of the underwater multi-port charging base station solves the energy problem of deep-sea long-term survey equipment, with poor energy sustainability and low charging efficiency.This approach will enable true continuous subsea operations in extremely dynamic ocean environments.Although the project is still a conceptual design and various sensors are still being experimented with, it is forward-looking and instructive for future applications.References1.Wang X., Lu J., Peng W., &Song L.,(2021) Accelerating the construction of marine "new infrastructure" and promoting high-quality development of marine industry,Science & Technology Review,39(16),pp.76-80.2.Qu, Feng-Chong, Lai. , Liu, J.-Z., Tu, X.-B., Jiang, Y.,(2021)'Research and Application of Key Technologies for Marine Internet of Things', Telecommunications Science, 37, (7), pp. 25-33.3.Tian Y., Yuan R.,&Li X.,(2018)'Design and experiment of deep-sea microcurrent power generation system', Acta Energiae Solaris Sinica,Journal of China Academy of Electronics and Information Technology, 39, (4), pp. 873-878.4.SubseaDockingStation(SDS).[Online].Available:https://www.bluelogic.no/news-and-media/subsea-docking-station-sds-.5.Abicht, D., Torvestad, J.C., Solheimsnes, P.A., and Stenevik, K.A., ‘Underwater Intervention Drone Subsea Control System’, in Proceedings of the OTC, 2020.6.Wang Y., &Tian F.,(2019)'Research on acoustic wave-based charging planning in underwater sensing networks',Journal of China Academy of Electronics and Information Technology,14(11),pp.1183-11877.Cruz, N.A., Matos, A.C., Almeida, R.M., and Ferreira, B.M.: ‘A lightweight docking station for a hovering AUV’, in Proceedings of the IEEE, 2017, pp. 1-7.