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Relevant bibliographies by topics / Homology modelling

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Academic literature on the topic 'Homology modelling'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 September 2023

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Journal articles on the topic "Homology modelling"

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Swindells, Mark B., and Janet M. Thornton. "Modelling by homology." Current Opinion in Structural Biology 1, no. 2 (April 1991): 219–23. http://dx.doi.org/10.1016/0959-440x(91)90064-z.

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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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Vincent Vidyasagar J, Tharun Kumar G, Ramesh M, and Akila C R. "Current review on homology modelling." International Journal of Pharmaceutical Research and Life Sciences 7, no. 2 (December 28, 2019): 30–33. http://dx.doi.org/10.26452/ijprls.v7i2.1338.

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The procheck synopsis of the model is considered, and the anolea chart is inspected. Presently a little arrangement of an obscure protein is taken, and its grouping arrangement is finished with the assistance of a layout. The swiss model workspace is utilized to at extended last model the structure of the obscure protein. The procheck outline and its anolea are inspected and contrasted and the structure of the known protein. The approval of the structure is assessed.

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Aszódi, Andrés, and William R. Taylor. "Homology modelling by distance geometry." Folding and Design 1, no. 5 (October 1996): 325–34. http://dx.doi.org/10.1016/s1359-0278(96)00048-x.

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BARRY, THOMAS R., and SHAWN DOONAN. "Homology modelling of yeast aspartate aminotransferase." Biochemical Society Transactions 22, no. 1 (February 1, 1994): 83S. http://dx.doi.org/10.1042/bst022083s.

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Domicevica, Laura, and Philip C. Biggin. "Homology modelling of human P-glycoprotein." Biochemical Society Transactions 43, no. 5 (October 1, 2015): 952–58. http://dx.doi.org/10.1042/bst20150125.

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P-glycoprotein (P-gp) is an ATP-binding cassette transporter that exports a huge range of compounds out of cells and is thus one of the key proteins in conferring multi-drug resistance in cancer. Understanding how it achieves such a broad specificity and the series of conformational changes that allow export to occur form major, on-going, research objectives around the world. Much of our knowledge to date has been derived from mutagenesis and assay data. However, in recent years, there has also been great progress in structural biology and although the structure of human P-gp has not yet been solved, there are now a handful of related structures on which homology models can be built to aid in the interpretation of the vast amount of experimental data that currently exists. Many models for P-gp have been built with this aim, but the situation is complicated by the apparent flexibility of the system and by the fact that although many potential templates exist, there is large variation in the conformational state in which they have been crystallized. In this review, we summarize how homology modelling has been used in the past, how models are typically selected and finally illustrate how MD simulations can be used as a means to give more confidence about models that have been generated via this approach.

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Zhekova, Hristina R., Igor Zdravkovic, Sergei Yu Noskov, Toshie Sakuma, Susanna C. Concilio, Ryan Johnson, Stephen J. Russell, and Kah-Whye Peng. "Homology Modelling of Sodium Iodide Symporter." Biophysical Journal 114, no. 3 (February 2018): 573a—574a. http://dx.doi.org/10.1016/j.bpj.2017.11.3137.

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Vlachakis, Dimitrios, Dimitrios Georgios Kontopoulos, and Sophia Kossida. "Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus." Computational and Mathematical Methods in Medicine 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/108910.

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Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.

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Boscott, P. E., G. J. Barton, and W. G. Richards. "Secondary structure prediction for modelling by homology." "Protein Engineering, Design and Selection" 6, no. 3 (1993): 261–66. http://dx.doi.org/10.1093/protein/6.3.261.

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Ghetti, Andrea, Martino Bolognesi, Fabio Cobianchi, and Carlo Morandi. "Modelling by homology of RNA binding domain." Molecular Biology Reports 14, no. 2-3 (1990): 87–88. http://dx.doi.org/10.1007/bf00360427.

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Dissertations / Theses on the topic "Homology modelling"

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Dalton, James Andrew Rupert. "The homology modelling of protein-ligand interactions." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515451.

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Asi, Azizah. "Homology modelling and simulations of the major facilitator superfamily transporters." Thesis, University of Oxford, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.724976.

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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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Anye, Valentine. "Structural analysis of induced mutagenesis A’ protein from mycobacterium tuberculosis and of a thermophillic GH9 cellulase." University of the Western Cape, 2014. http://hdl.handle.net/11394/4320.

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Masters of Science
The three-dimensional structures of proteins are important in understanding their function and interaction with ligands and other proteins. In this work, the structures of two proteins, ImuA’ from mycobacterium tuberculosis and GH9 C1 cellulase from a metagenomic library, were analysed using structural biological and modelling techniques. The gene encoding ImuA’ was amplified by two-step PCR, cloned, and expressed in E. coli. The recombinant ImuA’ produced was found to be largely insoluble. The insoluble protein was successfully solubilized in 8M urea but refolding the protein to its native structure was unsuccessful. By homology modelling, a 3D model of ImuA’ was obtained from a partly homologous protein RecA. In comparison to RecA, ImuA’ appears to lack some loop amino acids critical for DNA binding. Hence ImuA’ is postulated to not bind DNA. The second protein, GH9 C1 cellulase, was produced in E. coli. The protein was purified by chromatographic techniques and crystallized in a precipitant to protein ratio of 1:2 by hanging and sitting drop crystallization methods. The reservoir solution was made up of 15-30% (w/v) PEG 3350, 200 mM salt and 100 mM Tris-HCL pH 7.5-8.5. The protein crystals only diffracted x-rays to 4 å resolution which could not be used to obtain a crystal structure of the protein. The diffraction data, however, showed the crystal to be monoclinic with space group P2. Homology modelling revealed GH9 C1 cellulase to be a two domain protein with a smaller N-terminal Ig-like domain and a larger catalytic domain.The catalytic domain retains two ca2+ binding sites, which potentially stabilize the active site conformation and increase thermostability of the protein. Overall GH9 C1 cellulase is structurally similar to other GH9 cellulases, suggesting that its catalytic mechanism may be conserved.

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Nematollahi, Alireza. "Kynurenine Aminotransferases as Novel Targets in Neurodegenerative and Cognitive Disorders using Rational Drug Discovery." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/15985.

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This dissertation is premised on observations that kynurenine aminotransferase (KAT) isozymes play a role in neurodegenerative and cognitive disorders and has considered the probable mechanisms of action of inhibitors. This thesis used rational drug discovery in the design of novel reversible human KAT-2 inhibitors. This work is presented in publication format with six chapters. Chapter 1 includes two published papers of which the first article is about the evolution of antipsychotic drugs used in the clinic to overcome both positive and negative symptoms of schizophrenia with an emphasis on the main pharmacophore features of these drugs, and the second article is a review of KATs and their existing inhibitors. Chapter 2 presents the structural features of KAT-3 with observations on its inhibition using molecular modeling and computational studies. Chapter 3 investigates the expression, purification and crystallization of human KAT-2. Chapter 4 considers the crystal structure of human KAT-2 and properties of the active site of this enzyme, which relates to the mechanism of action of the KAT isozymes. Chapter 5 presents the design and synthesis of a novel reversible inhibitor of human KAT-2, a promising lead as assessed by an HPLC-based bioassay, as well as a study of the binding affinity by the surface plasmon resonance technique to probe further its probable mechanism of action. The final chapter, Chapter 6, summarizes the results of this research with suggestions for possible future research directions.

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Kroon, Matthys Christoffel. "High-throughput modelling and structural investigation of cysteine protease complexes with protein inhibitors." Thesis, Rhodes University, 2013. http://hdl.handle.net/10962/d1001619.

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The papain-like cysteine protease family (C1 proteases) is highly important because of its involvement in research and industrial applications and its role in various human diseases. Protein inhibitors are an important aspect of C1 protease biology and are relevant to its clinical, industrial and research importance. To study the interaction between the proteases and the inhibitors it is very useful to have accurate structural models of the protease-inhibitor complexes. To this end, a high-throughput pipeline for modelling complexes of papain-like cysteine proteases and protein inhibitors was implemented and tested (Tastan Bishop & Kroon, 2011). The pipeline utilizes a novel technique for obtaining modelling templates by using superpositioning to combine coordinates from separate experimental structures. To test the pipeline, models of complexes with known structures (test set) were modelled using many different templates and the resultant models evaluated to compare the quality of the different templates. It was found that use of the new technique to obtain templates did not introduce significant errors, while allowing closer homologs to be used for modelling - leading to more accurate models. The test set models were also used to evaluate certain steps of the modelling protocol. The effect of Rosetta energy minimization on model accuracy and the use of Rosetta energy and DOPE Z-score values to identify accurate models were investigated. Several complexes were then modelled using the best available templates according to criteria informed by the previous results. A website was built that allows a user to download any of the metrics or models produced in the study. This website is accessible at http://rubi.ru.ac.za/cpmdb

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Pereira, Ana Catarina da Silva. "Structural investigation of the Bacillus subtilis morphogenic factor RodZ." Master's thesis, Faculdade de Ciências e Tecnologia, 2013. http://hdl.handle.net/10362/11072.

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A thesis to obtain a Master degree in Structural and Functional Biochemistry
RodZ is a protein widely conserved in bacteria and a core component of the morphogenic apparatus of the cell. It is known to be required for assembly of the bacterial actin homologue, MreB, that controls cell wall synthesis and cell shape. The domain organization of RodZ consists of a well-conserved N-terminal (RodZn) with helix-turn-helix motif (HTH), a conserved transmembrane domain, and a conserved C-terminal domain (RodZc). RodZn, located in the cytoplasm, has been shown to interact with MreB actin-homologue by x-ray studies in T. maritima. However, the structure of RodZn from gram-positive B. subtilis showed low homology with the published one from gram-negative T. maritima. Here we present the solution structure of RodZn from B. subtilis determined for the first time, by NMR spectroscopy. Compared to previous structural data obtained from the crystallized RodZn from T. maritima and more recently from S. aureus, several differences could be observed, namely the length of the alpha-helices and the presence of an extended coil. Interaction studies were preformed between RodZn domain and MreB from which no significant results could be extrapolated. Since HTH motif is frequently associated with DNA interaction, the involvement of RodZn in DNA organization is being investigated. At the same time, RodZc domain, which structure has never been reported, was subject of study. Bioinformatic, biophysical and biochemical methodologies were employed to study this domain. A model based in a pseudo-ab initio methodology was built, revealing an Ig-like fold. The Ig superfamily is a large group of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. Therefore, RodZ is thought to be a protein that establishes a link between the inner side of the cell membrane and the outer side, promoting spatiotemporal coordination between peptidoglycan synthesis and cell division.

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Muhammad, Sayyed Auwn. "Probabilistic Modelling of Domain and Gene Evolution." Doctoral thesis, KTH, Beräkningsvetenskap och beräkningsteknik (CST), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-191352.

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Phylogenetic inference relies heavily on statistical models that have been extended and refined over the past years into complex hierarchical models to capture the intricacies of evolutionary processes. The wealth of information in the form of fully sequenced genomes has led to the development of methods that are used to reconstruct the gene and species evolutionary histories in greater and more accurate detail. However, genes are composed of evolutionary conserved sequence segments called domains, and domains can also be affected by duplications, losses, and bifurcations implied by gene or species evolution. This thesis proposes an extension of evolutionary models, such as duplication-loss, rate, and substitution, that have previously been used to model gene evolution, to model the domain evolution. In this thesis, I am proposing DomainDLRS: a comprehensive, hierarchical Bayesian method, based on the DLRS model by Åkerborg et al., 2009, that models domain evolution as occurring inside the gene and species tree. The method incorporates a birth-death process to model the domain duplications and losses along with a domain sequence evolution model with a relaxed molecular clock assumption. The method employs a variant of Markov Chain Monte Carlo technique called, Grouped Independence Metropolis-Hastings for the estimation of posterior distribution over domain and gene trees. By using this method, we performed analyses of Zinc-Finger and PRDM9 gene families, which provides an interesting insight of domain evolution. Finally, a synteny-aware approach for gene homology inference, called GenFamClust, is proposed that uses similarity and gene neighbourhood conservation to improve the homology inference. We evaluated the accuracy of our method on synthetic and two biological datasets consisting of Eukaryotes and Fungal species. Our results show that the use of synteny with similarity is providing a significant improvement in homology inference.

QC 20160904

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Fischer, Juliane [Verfasser], Birgit [Akademischer Betreuer] Dräger, Wolfgang [Akademischer Betreuer] Brandt, and Dietrich [Akademischer Betreuer] Ober. "Homology modelling, virtual screening and evolutionary analyses of plant enzymes metabolising putrescine / Juliane Fischer. Betreuer: Birgit Dräger ; Wolfgang Brandt ; Dietrich Ober." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2015. http://d-nb.info/1077768095/34.

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Riemann, Ralph Nico [Verfasser]. "Development of potential scaling methods to improve prediction of loops and binding interfaces at homology modelling and docking / Ralph Nico Riemann." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2008. http://d-nb.info/1034788132/34.

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Books on the topic "Homology modelling"

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Limited, Oxford Molecular. Cameleon: Protein sequence homology modelling system : user's guide : [version 2.0]. Oxford: Oxford Molecular, 1992.

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Book chapters on the topic "Homology modelling"

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Strasser, Andrea, and Hans-Joachim Wittmann. "Sequence Alignment and Homology Modelling." In Modelling of GPCRs, 13–28. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4596-4_3.

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Pirard, Bernard, and Russell C. Viner. "Homology Modelling of Drosophila Melanogaster and Electrophorus Eel Acetylcholinesterases." In Structure and Function of Cholinesterases and Related Proteins, 451. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4899-1540-5_127.

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Sahu, Nivedita, Anirudh Nelabhotla, and Pradhan Nityananda. "Structure and Gas Diffusion Path Analysis of Hydrogenase Enzymes by Homology Modelling." In Microbial Biotechnology, 277–93. Toronto ; New Jersey : Apple Academic Press, 2015.: Apple Academic Press, 2017. http://dx.doi.org/10.1201/b19978-18.

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Folkers, Gerd. "Integrated Homology Modelling and X-Ray Study of Herpes Simplex Virus I Thymidine Kinase." In Structure-Based Drug Design, 271–83. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_24.

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Saddala, Madhu Sudhana, and A. Usha Rani. "Homology Modelling, Structure-Based Pharmacophore Modelling, High-Throughput Virtual Screening and Docking Studies of L-Type Calcium Channel for Cadmium Toxicity." In Translational Bioinformatics and Its Application, 153–75. Dordrecht: Springer Netherlands, 2017. http://dx.doi.org/10.1007/978-94-024-1045-7_7.

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Renouf, David V., and Elizabeth F. Hounsell. "Molecular Modelling of Glycoproteins by Homology with Non-Glycosylated Protein Domains, Computer Simulated Glycosylation and Molecular Dynamics." In Advances in Experimental Medicine and Biology, 37–45. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-1885-3_4.

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Sarkar, Indrani. "To Compare the Active Sites of a Series of Astacin Family Proteases by Multiple Sequence Alignment and Homology Modelling Methods." In Computational Advancement in Communication Circuits and Systems, 145–50. New Delhi: Springer India, 2015. http://dx.doi.org/10.1007/978-81-322-2274-3_18.

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Pitman, Melissa R., and R. Ian Menz. "Methods for Protein Homology Modelling." In Applied Mycology and Biotechnology, 37–59. Elsevier, 2006. http://dx.doi.org/10.1016/s1874-5334(06)80005-5.

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Chakraborty, Hirak Jyoti, Aditi Gangopadhyay, Sayak Ganguli, and Abhijit Datta. "Protein Structure Prediction." In Advances in Bioinformatics and Biomedical Engineering, 48–79. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-2607-0.ch003.

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The great disagreement between the number of known protein sequences and the number of experimentally determined protein structures indicate an enormous necessity of rapid and accurate protein structure prediction methods. Computational techniques such as comparative modeling, threading and ab initio modelling allow swift protein structure prediction with sufficient accuracy. The three phases of computational protein structure prediction comprise: the pre-modelling analysis phase, model construction and post-modelling refinement. Protein modelling is primarily comparative or ab initio. Comparative or template-based methods such as homology and threading-based modelling require structural templates for constructing the structure of a target sequence. The ab initio is a template-free modelling approach which proceeds by satisfying various physics-based and knowledge-based parameters. The chapter will elaborate on the three phases of modelling, the programs available for performing each, issues, possible solutions and future research areas.

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Chakraborty, Hirak Jyoti, Aditi Gangopadhyay, Sayak Ganguli, and Abhijit Datta. "Protein Structure Prediction." In Biotechnology, 156–84. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-8903-7.ch007.

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The great disagreement between the number of known protein sequences and the number of experimentally determined protein structures indicate an enormous necessity of rapid and accurate protein structure prediction methods. Computational techniques such as comparative modeling, threading and ab initio modelling allow swift protein structure prediction with sufficient accuracy. The three phases of computational protein structure prediction comprise: the pre-modelling analysis phase, model construction and post-modelling refinement. Protein modelling is primarily comparative or ab initio. Comparative or template-based methods such as homology and threading-based modelling require structural templates for constructing the structure of a target sequence. The ab initio is a template-free modelling approach which proceeds by satisfying various physics-based and knowledge-based parameters. The chapter will elaborate on the three phases of modelling, the programs available for performing each, issues, possible solutions and future research areas.

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Conference papers on the topic "Homology modelling"

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Sapundzhi, Fatima, Tatyana Dzimbova, Nevena Pencheva, and Peter Milanov. "Homology Modelling and Evaluation of the CannabinoidReceptor Type 2." In 35th European Peptide Symposium. Prompt Scientific Publishing, 2018. http://dx.doi.org/10.17952/35eps.2018.327.

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Bazlan, Nur Hamizah Noor, Norfatimah Mohamed Yunus, and Mohd Fakharul Zaman Raja Yahya. "In Silico analysis and homology modelling of carbohydrate metabolic enzymes from Corynebacterium Pseudotuberculosis." In 5TH INTERNATIONAL CONFERENCE ON ELECTRICAL, ELECTRONIC, COMMUNICATION AND CONTROL ENGINEERING (ICEECC 2021). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0137771.

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Cabrera, H. S., I. C. Medina, and L. L. Tayo. "In silico screening of inhibitors of p53-MDM2 protein complex through homology modelling and molecular docking." In 4TH ELECTRONIC AND GREEN MATERIALS INTERNATIONAL CONFERENCE 2018 (EGM 2018). Author(s), 2018. http://dx.doi.org/10.1063/1.5080888.

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Reports on the topic "Homology modelling"

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Avdjieva, Irena, Ivan Terziyski, Gergana Zahmanova, Valeria Simeonova, Ognyan Kulev, Evgeny Krustev, Milko Krachunov, Maria Nisheva, and Dimitar Vassilev. Homology Based Computational Modelling of Hepatitis-E Viral Fusion Capsid Protein. Balkan, Black sea and Caspian sea Regional Network for Space Weather Studies, March 2019. http://dx.doi.org/10.7546/crabs.2019.03.10.

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