Computation and Visualization of Protein Ligand Graphs

Abstract

Fig. 2 a) Overlapping collision spheres of two residues. A, atom; R, protein residue or ligand molecule. b) Data sources and output of VPLG. The PDB files containing 3D atomic coordinates are downloaded from the RCSB PDB and DSSP is used to assign SSEs to each protein residue. VPLG reads both the PDB and DSSP files and uses them to generate a protein graph file and a bitmap or vector image of the protein graph. Optionally, statistics and the graph can also be written to a database. 1) 2)