Relevant bibliographies by topics / Protein loop modelling

Academic literature on the topic 'Protein loop modelling'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Protein loop modelling"

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Michalsky, E., A. Goede, and R. Preissner. "Loops In Proteins (LIP)--a comprehensive loop database for homology modelling." Protein Engineering Design and Selection 16, no. 12 (December 1, 2003): 979–85. http://dx.doi.org/10.1093/protein/gzg119.

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Thanki, N., J. P. Zeelen, M. Mathieu, R. Jaenicke, R. A. Abagyan, R. K. Wierenga, and W. Schliebs. "Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop." Protein Engineering Design and Selection 10, no. 2 (February 1, 1997): 159–67. http://dx.doi.org/10.1093/protein/10.2.159.

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MacDonald, James T., Lawrence A. Kelley, and Paul S. Freemont. "Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling." PLoS ONE 8, no. 6 (June 18, 2013): e65770. http://dx.doi.org/10.1371/journal.pone.0065770.

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Sowdhamini, R., C. Ramakrishnan, and P. Balaram. "Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I." "Protein Engineering, Design and Selection" 6, no. 8 (1993): 873–82. http://dx.doi.org/10.1093/protein/6.8.873.

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Tata, Rolland B., Ali F. Alsulami, Olivier Sheik Amamuddy, Tom L. Blundell, and Özlem Tastan Bishop. "Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds." International Journal of Molecular Sciences 23, no. 3 (January 28, 2022): 1514. http://dx.doi.org/10.3390/ijms23031514.

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The presence of protein structures with atypical folds in the Protein Data Bank (PDB) is rare and may result from naturally occurring knots or crystallographic errors. Proper characterisation of such folds is imperative to understanding the basis of naturally existing knots and correcting crystallographic errors. If left uncorrected, such errors can frustrate downstream experiments that depend on the structures containing them. An atypical fold has been identified in P. falciparum dihydrofolate reductase (PfDHFR) between residues 20–51 (loop 1) and residues 191–205 (loop 2). This enzyme is key to drug discovery efforts in the parasite, necessitating a thorough characterisation of these folds. Using multiple sequence alignments (MSA), a unique insert was identified in loop 1 that exacerbates the appearance of the atypical fold-giving it a slipknot-like topology. However, PfDHFR has not been deposited in the knotted proteins database, and processing its structure failed to identify any knots within its folds. The application of protein homology modelling and molecular dynamics simulations on the DHFR domain of P. falciparum and those of two other organisms (E. coli and M. tuberculosis) that were used as molecular replacement templates in solving the PfDHFR structure revealed plausible unentangled or open conformations of these loops. These results will serve as guides for crystallographic experiments to provide further insights into the atypical folds identified.
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Studer, Gabriel, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner, and Torsten Schwede. "ProMod3—A versatile homology modelling toolbox." PLOS Computational Biology 17, no. 1 (January 28, 2021): e1008667. http://dx.doi.org/10.1371/journal.pcbi.1008667.

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Computational methods for protein structure modelling are routinely used to complement experimental structure determination, thus they help to address a broad spectrum of scientific questions in biomedical research. The most accurate methods today are based on homology modelling, i.e. detecting a homologue to the desired target sequence that can be used as a template for modelling. Here we present a versatile open source homology modelling toolbox as foundation for flexible and computationally efficient modelling workflows. ProMod3 is a fully scriptable software platform that can perform all steps required to generate a protein model by homology. Its modular design aims at fast prototyping of novel algorithms and implementing flexible modelling pipelines. Common modelling tasks, such as loop modelling, sidechain modelling or generating a full protein model by homology, are provided as production ready pipelines, forming the starting point for own developments and enhancements. ProMod3 is the central software component of the widely used SWISS-MODEL web-server.
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Jezierski, G., and M. Pasenkiewicz-Gierula. "The effect of the Glu342Lys mutation in alpha1-antitrypsin on its structure, studied by molecular modelling methods." Acta Biochimica Polonica 48, no. 1 (March 31, 2001): 65–75. http://dx.doi.org/10.18388/abp.2001_5112.

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The structure of native alpha1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a beta-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the beta structure. The most common mutation in the protein, resulting in its inactivation, is Glu342-->Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of alpha1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of alpha1-antitrypsin.
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Collura, V. P., P. J. Greaney, and B. Robson. "A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603." "Protein Engineering, Design and Selection" 7, no. 2 (1994): 221–33. http://dx.doi.org/10.1093/protein/7.2.221.

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Huang, Qi, Monika Tokmina-Lukaszewska, Lewis E. Johnson, Hayden Kallas, Bojana Ginovska, John W. Peters, Lance C. Seefeldt, Brian Bothner, and Simone Raugei. "Mechanical coupling in the nitrogenase complex." PLOS Computational Biology 17, no. 3 (March 4, 2021): e1008719. http://dx.doi.org/10.1371/journal.pcbi.1008719.

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The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.
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Ledoux, Julie, Maxim Stolyarchuk, Enki Bachelier, Alain Trouvé, and Luba Tchertanov. "Human Vitamin K Epoxide Reductase as a Target of Its Redox Protein." International Journal of Molecular Sciences 23, no. 7 (March 31, 2022): 3899. http://dx.doi.org/10.3390/ijms23073899.

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Human vitamin K epoxide reductase (hVKORC1) enzymatic activity requires an initial activation by a specific redox protein, a less studied step in the hVKORC1 vital cycle. Significant steric conditions must be met by enzymes, being that to adapt their configurations is mandatory for hVKORC1 activation. We studied, by molecular dynamics (MD) simulations, the folding and conformational plasticity of hVKORC1 in its inactive (fully oxidised) state using available structures, crystallographic and from de novo modelling. According to the obtained results, hVKORC1 is a modular protein composed of the stable transmembrane domain (TMD) and intrinsically disordered luminal (L) loop, possessing the great plasticity/adaptability required to perform various steps of the activation process. The docking (HADDOCK) of Protein Disulfide Isomerase (PDI) onto different hVKORC1 conformations clearly indicated that the most interpretable solutions were found on the target closed L-loop form, a prevalent conformation of hVKORC1’s oxidised state. We also suggest that the cleaved L-loop is an appropriate entity to study hVKORC1 recognition/activation by its redox protein. Additionally, the application of hVKORC1 (membrane protein) in aqueous solution is likely to prove to be very useful in practice in either in silico studies or in vitro experiments.
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Dissertations / Theses on the topic "Protein loop modelling"

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Marks, Claire. "Hybrid methods for protein loop modelling." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:5c0d6343-480e-4de5-a99f-3ca9b5d065c5.

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Loops are often vital for protein function, and therefore accurate prediction of their structures is highly desirable. A particularly important example is the H3 loop of antibodies. Antibodies are proteins of the immune system that are able to bind to a huge variety of different substances, in order to initiate their removal from the body. The binding characteristics of an antibody are mainly determined by the six loops, or complementarity determining regions, that make up their binding site. The most important of these is the H3 loop - however, since it is extremely variable in structure, the accuracy of H3 structure prediction is often poor. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations; and ab initio, where conformations are generated computationally. In this thesis, we test the ability of such methods to predict H3 structures using one of each: the previously published, knowledge-based algorithm FREAD; and our own new ab initio method MECHANO. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. We describe the development of a novel algorithm, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Finally we look at protein flexibility, by identifying loops for which there are multiple structures deposited in the PDB. We examine the outcome of performing structure prediction on loops with varying amounts of flexibility, and investigate differences between those loops that show a high degree of structural variability and those that do not.
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Jones, Martin Lionel. "Analysing loop selection criteria in homology modelling of proteins using an object-oriented database." Thesis, University of Aberdeen, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387153.

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One of the most difficult problems in modern biochemistry is that of accurately predicting a protein's three dimensional structure from its sequence (the protein folding problem). This structure is essential for a proper understanding of how a protein functions. As experimental derivation of a protein's structure is far more time consuming than deriving a protein's sequence, prediction of structure from sequence is an important goal for many protein biochemists; several methods have been suggested for this. Given a protein of known structure of similar sequence to the protein you wish to model homology modelling is the method most likely to produce a fairly good model. In this work a tool was produced for examining the various stages of homology modelling and analysing how well various method for carrying out these stages perform. The tool produced consists of an object-oriented database of protein structures and testbed software written in a mixture of PROLOG and DAPLEX. Tests were carried out using this software to examine the predictivity of various guidelines suggested in the literature for the loop selection stage of cut and paste homology modelling. The results of these tests produced surprising new information on the relative importance of different factors which may be used to choose between candidate fragments for the variable regions of a protein being modelled. The results of the application of these automated modelling methods were then compared with a short series of modelling tests using human modellers in an attempt to measure how the usual modelling procedures using 'hand and eye' compare with automated measures. Finally the results of the tests carried out were used to guide the production of a model of a previously unmodelled serine proteinase.
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Rea, Jonathan R. "ARCUS : development of a hierarchical ab initio protein loop modelling methodology." Thesis, University of Bristol, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.446156.

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Kelm, Sebastian. "Structural modelling of transmembrane domains." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:b4c9fba9-ee25-469b-8baf-b7c1d70c9d05.

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Membrane proteins represent about one third of all known vertebrate proteins and over half of the current drug targets. Knowledge of their three-dimensional (3D) structure is worth millions of pounds to the pharmaceutical industry. Yet experimental structure elucidation of membrane proteins is a slow and expensive process. In the absence of experimental data, computational modelling tools can be used to close the gap between the numbers of known protein sequences and structures. However, currently available structure prediction tools were developed with globular soluble proteins in mind and perform poorly on membrane proteins. This thesis describes the development of a modelling approach able to predict accurately the structure of transmembrane domains of proteins. In this thesis we build a template-based modelling framework especially for membrane proteins, which uses membrane protein-specific information to inform the modelling process.Firstly, we develop a tool to accurately determine a given membrane protein structure's orientation within the membrane. We offer an analysis of the preferred substitution patterns within the membrane, as opposed to non-membrane environments, and how these differences influence the structures observed. This information is then used to build a set of tools that produce better sequence alignments of membrane proteins, compared to previously available methods, as well as more accurate predictions of their 3D structures. Each chapter describes one new piece of software or information and uses the tools and knowledge described in previous chapters to build up to a complete accurate model of a transmembrane domain.
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Fernandez-Carmona, Juan. "Modelling protein backbone loops using the Monte Carlo method." Thesis, University of Southampton, 2009. https://eprints.soton.ac.uk/173851/.

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Novel methods that perform local moves such as the gaussian bias or Con- certed Rotation with Angles, increase the exploration of the conformational phase space. These methods have been applied successfully to small systems, and have proved to be more efficient than the classical Monte Carlo method. The main aim of my work was to study and include backbone moves for proteins, such as the Concerted Rotation with Angle (CRA) and the gaussian bias in the ProtoMS package. The CRA was then applied to several systems of biological interest to compute relative binding free energies and conformational changes to obtain insights into the binding mode and system flexibility. The CRA algorithm has been used to sample biological systems such as lysozyme L99A mutant, Bcr-Abl kinases and PDE5 phosphodiesterase and led to increased sampling of the backbone and more precise free energy results.
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Book chapters on the topic "Protein loop modelling"

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Wu, Mengzhe, Jakob Kjøbsted Huusom, Krist V. Gernaey, and Ulrich Krühne. "Modelling and simulation of a U-loop Reactor for Single Cell Protein Production." In Computer Aided Chemical Engineering, 1287–92. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-444-63428-3.50219-8.

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Luttmann, R., A. Munack, and M. Thoma. "Mathematical Modelling, Parameter Identification and Adaptive Control of Single Cell Protein Processes in Tower Loop Bioreactors." In Agricultural Feedstock and Waste Treatment and Engineering, 95–206. De Gruyter, 1985. http://dx.doi.org/10.1515/9783112587423-004.

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Reinecke, Ines, Franziska Bathelt, Martin Sedlmayr, and Andreas Kühn. "Pharmaceutical Feedback Loop – A Concept to Improve Prescription Safety and Data Quality." In Studies in Health Technology and Informatics. IOS Press, 2022. http://dx.doi.org/10.3233/shti220910.

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Data quality is essential for utilizing real world data (RWD) in scientific context. Based on drug prescriptions in a hospital information system (HIS), algorithms performed a mapping of unstructured drug data to ATC codes. Visualization of the resulting distribution of structured to unstructured data based on ATC codes was created and used to explore a defined limitation of the current drug prescription highlighting the example of proton pump inhibitors. As a second step, a generalization of this approach was inductively created. As result we were able to identify 4 crucial steps for a feedback loop framework: The first step being the actual use of the HIS by clinician for drug prescription, second the processing of the entered unstructured and structured data and performing automatic analyses and visualization of the resulting distributions. The third step included an interdisciplinary expert evaluation of the data distribution followed by the fourth step, consisting of feedback to the stakeholders and generating actions as teaching or re-modelling of the system incorporating the actual learning process. The presented approach represents a continuously learning system based on RWD, although it is limited by analyzing the distribution of mapped unstructured text to ATC codes and therefore does not allow to analyze free text not mapped to ATC codes (false negatives). Future work will focus on the evaluation of this approach to analyze the impact on prescription data quality and the potential improvement on patient safety in general.
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