SynthPDB

SynthPDB synthesizes and visualizes information from a set of Protein Data Bank files of similar sequences but different protein contexts. It can read sequence alignment files in Clustal Omega format and uses this information to align PDB files both in sequence and in space.

A test example is given using an alignment of all known human bromodomains: highly important protein domains that recognize acetylated histone proteins, and are essential to epigenetic regulation and cell differentiation. The sequence alignment was conducted on 255 known human bromodomain sequence fragments, which can occur multiple times in a single protein sequence (such as BRD4). Information such as ligand position, amino acid shielding and accessibility is obtained for a set of 283 PDB files in this example.