On the Perception of Molecules from 3D Atomic Coordinates
- 19 January 2005
- journal article
- Published by American Chemical Society (ACS) in Journal of Chemical Information and Modeling
- Vol. 45 (2), 215-221
- https://doi.org/10.1021/ci049915d
Abstract
A method is presented for perceiving chemical types of atoms in molecules given 3D atomic coordinates and element identities. The method assigns hybridizations, bond orders, and formal charges for structures whether hydrogen atoms are present. The Maximum Weighted Matching algorithm for nonbipartite graphs is used to assign bond orders with weights derived from statistics of a large collection of organic molecules. Results form tests on a collection of functional groups, heterocycles, entries from the Protein Data Bank, and Cambridge Structural Database as well as a comparison to other methods, are presented and discussed.This publication has 5 references indexed in Scilit:
- Databases for Protein–Ligand ComplexesActa Crystallographica Section D-Biological Crystallography, 1998
- BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein DatabankJournal of Chemical Information and Computer Sciences, 1997
- 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 DatabaseJournal of Chemical Information and Computer Sciences, 1993
- Automatic assignment of chemical connectivity to organic molecules in the Cambridge Structural DatabaseJournal of Chemical Information and Computer Sciences, 1992
- The development of versions 3 and 4 of the Cambridge Structural Database SystemJournal of Chemical Information and Computer Sciences, 1991