An improved approach to the analysis of drug-protein binding by distance geometry

Amiram Goldblum*, Thomas Kieber-Emmons, Robert Rein

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard CC distance representations.

Original languageAmerican English
Pages (from-to)415-428
Number of pages14
JournalJournal of Molecular Structure: THEOCHEM
Issue number3-4
StatePublished - Jan 1986

Bibliographical note

Funding Information:
This study was supported, in part, by a research grant from the National Aeronautics and Space Administration (NSG-7305), and pursuant, in part, to a contract with the National Foundation for Cancer Research . The authors would like to thank Joseph McDonald for providing technical assistance, Dr . Subhashini Srinivasan for developing the graphics programs in conjunction with an Evans and Sutherland PS 300 graphics computer, Masayuki Shibata for his assistance with the plotter programs, and Deborah Raye for her assistance in the preparation of the manuscript .


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