Abstract
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.
Highlights
High-throughput methods in proteomics have resulted in substantial information on protein-protein interactions and identification of the components of large protein complexes [1]
We have developed a downloadable program, BioAssemblyModeler or BAM that provides for the modeling of the structures of protein homo- and heterooligomers
(8) The model is built by clicking on a button that copies the template backbone to a new PDB file with the sequence numbered according to the edited alignments, and clicking another button to run our side-chain prediction program SCWRL4 [13], which models all of the mutated side chains with a backbone-dependent rotamer library [19], preserving the rotamers of residues that are identical in the target and template sequences
Summary
High-throughput methods in proteomics have resulted in substantial information on protein-protein interactions and identification of the components of large protein complexes [1]. BAM assigns Pfam domains to the queries and finds templates and the content of their biological assemblies from our regularly updated PDBfam database [11].
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