COMPARISON OF CONFORMATIONS OF SMALL-MOLECULE STRUCTURES FROM THE PROTEIN DATA-BANK WITH THOSE GENERATED BY CONCORD, COBRA, CHEMDBS-3D, AND CONVERTER AND THOSE EXTRACTED FROM THE CAMBRIDGE STRUCTURAL DATABASE

This paper explores the ability of the 2D-3D structure conversion packages Concord, Cobra, ChemDBS-3D, and Converter to generate the structures of bound small molecules and compares their conformations with those in ligand complex crystal entries in the Brookhaven Protein Data Bank. ChemDBS-3D is limited by the size of structure that it can handle in its database environment and can only process 62% of the structures, but when these structures are compared with the ligand structures, they are found to most closely approximate the bound conformation. However Converter can be considered to perform better as it can convert 100% of the structures from input 2D diagrams, and its conformations are a good match in most cases. Concord performs well in converting 92% of the structures from input SMILES strings, and the conformations that it produces are good in many cases. The version of Cobra used (1.1) was found to have many problems, which limited its usefulness in this study; Cobra correctly processed only 48% of the structures. Comparisons of the conformations of some of the ligands with entries from the Cambridge Structural Database have mixed success.