BioAssemblyModeler (BAM): user-friendly homology modeling of protein homo- and heterooligomers.

ABSTRACT:

Unlabelled

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 co

SUBMITTER: Shapovalov MV 

PROVIDER: S-EPMC4055448 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature