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...

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Bibliographic Details
Published in:PloS one 2014-06, Vol.9 (6), p.e98309-e98309
Main Authors: Shapovalov, Maxim V, Wang, Qiang, Xu, Qifang, Andrake, Mark, Dunbrack, Jr, Roland L
Format: Article
Language:English
Subjects:
Acids
Alignment
Animals
Assemblies
Assembly
Banks (Finance)
Bioinformatics
Biology and Life Sciences
Cancer
Computer and Information Sciences
Dimers
Graphical user interface
Homology
Humans
Linux
Medical research
Modelling
Mutation
Navigation systems
Protein structure
Protein Subunits - chemistry
Proteins
Protocol (computers)
Relational data bases
Secondary structure
Sequence Alignment - methods
Sequence Analysis, Protein - methods
Sequence Homology, Amino Acid
Sequences
Software
Three dimensional models
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Description
Summary: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. http://dunbrack.fccc.edu/BAM.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0098309