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BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers
Many if not most proteins function in oligomeric assemblies of one or more protein sequences. The Protein Data Bank provides coordinates for biological assemblies for each entry, at least 60% of which are dimers or larger assemblies. BioAssemblyModeler (BAM) is a graphical user interface to the basi...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055448/ https://www.ncbi.nlm.nih.gov/pubmed/24922057 http://dx.doi.org/10.1371/journal.pone.0098309 |
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author | Shapovalov, Maxim V. Wang, Qiang Xu, Qifang Andrake, Mark Dunbrack, Roland L. |
author_facet | Shapovalov, Maxim V. Wang, Qiang Xu, Qifang Andrake, Mark Dunbrack, Roland L. |
author_sort | Shapovalov, Maxim V. |
collection | PubMed |
description | Many if not most proteins function in oligomeric assemblies of one or more protein sequences. The Protein Data Bank provides coordinates for biological assemblies for each entry, at least 60% of which are dimers or larger assemblies. BioAssemblyModeler (BAM) is a graphical user interface to the basic steps in homology modeling of protein homooligomers and heterooligomers from the biological assemblies provided in the PDB. BAM takes as input up to six different protein sequences and begins by assigning Pfam domains to the target sequences. The program utilizes a complete assignment of Pfam domains to sequences in the PDB, PDBfam (http://dunbrack2.fccc.edu/protcid/pdbfam), to obtain templates that contain any or all of the domains assigned to the target sequence(s). The contents of the biological assemblies of potential templates are provided, and alignments of the target sequences to the templates are produced with a profile-profile alignment algorithm. BAM provides for visual examination and mouse-editing of the alignments supported by target and template secondary structure information and a 3D viewer of the template biological assembly. Side-chain coordinates for a model of the biological assembly are built with the program SCWRL4. A built-in protocol navigation system guides the user through all stages of homology modeling from input sequences to a three-dimensional model of the target complex. Availability: http://dunbrack.fccc.edu/BAM. |
format | Online Article Text |
id | pubmed-4055448 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-40554482014-06-18 BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers Shapovalov, Maxim V. Wang, Qiang Xu, Qifang Andrake, Mark Dunbrack, Roland L. PLoS One Research Article Many if not most proteins function in oligomeric assemblies of one or more protein sequences. The Protein Data Bank provides coordinates for biological assemblies for each entry, at least 60% of which are dimers or larger assemblies. BioAssemblyModeler (BAM) is a graphical user interface to the basic steps in homology modeling of protein homooligomers and heterooligomers from the biological assemblies provided in the PDB. BAM takes as input up to six different protein sequences and begins by assigning Pfam domains to the target sequences. The program utilizes a complete assignment of Pfam domains to sequences in the PDB, PDBfam (http://dunbrack2.fccc.edu/protcid/pdbfam), to obtain templates that contain any or all of the domains assigned to the target sequence(s). The contents of the biological assemblies of potential templates are provided, and alignments of the target sequences to the templates are produced with a profile-profile alignment algorithm. BAM provides for visual examination and mouse-editing of the alignments supported by target and template secondary structure information and a 3D viewer of the template biological assembly. Side-chain coordinates for a model of the biological assembly are built with the program SCWRL4. A built-in protocol navigation system guides the user through all stages of homology modeling from input sequences to a three-dimensional model of the target complex. Availability: http://dunbrack.fccc.edu/BAM. Public Library of Science 2014-06-12 /pmc/articles/PMC4055448/ /pubmed/24922057 http://dx.doi.org/10.1371/journal.pone.0098309 Text en © 2014 Shapovalov et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Shapovalov, Maxim V. Wang, Qiang Xu, Qifang Andrake, Mark Dunbrack, Roland L. BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers |
title | BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers |
title_full | BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers |
title_fullStr | BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers |
title_full_unstemmed | BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers |
title_short | BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers |
title_sort | bioassemblymodeler (bam): user-friendly homology modeling of protein homo- and heterooligomers |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055448/ https://www.ncbi.nlm.nih.gov/pubmed/24922057 http://dx.doi.org/10.1371/journal.pone.0098309 |
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