Cavity search: an algorithm for the isolation and display of cavity-like binding regions

Journal of Computer-aided Molecular Design
C M Ho, G R Marshall

Abstract

A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show both electrostatic and steric interactions between the protein cavity and a bound ligand.

References

Jan 1, 1977·Annual Review of Biophysics and Bioengineering·F M Richards
Dec 1, 1989·Journal of Molecular Graphics·R VoorintholtW G Hol
Jun 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·P K WeinerP A Kollman
Oct 25, 1982·Journal of Molecular Biology·I D KuntzT E Ferrin
Apr 1, 1986·Journal of Computational Chemistry·Scott J WeinerDavid A Case

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Citations

Oct 7, 1998·Protein Science : a Publication of the Protein Society·J LiangC Woodward
Feb 1, 1995·Journal of Computer-aided Molecular Design·C M Ho, G R Marshall
Dec 1, 1993·Biophysical Journal·O S SmartB A Wallace
Mar 12, 2002·Journal of Molecular Graphics & Modelling·Felix Deanda, Robert S Pearlman
Aug 6, 1999·Journal of Molecular Graphics & Modelling·M Stahl, H J Böhm
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Deok-Soo KimJong Bhak
Feb 11, 2005·Bioinformatics·Alasdair T R Laurie, Richard M Jackson
Feb 3, 2007·Bioinformatics·George Nicola, Ilya A Vakser
Oct 9, 2007·Bioinformatics·Min HuQunsheng Peng
May 18, 2011·Nucleic Acids Research·Kuan Pern TanM S Madhusudhan
Sep 21, 2007·Chemistry Central Journal·Martin WeiselGisbert Schneider
Aug 2, 2008·Biological & Pharmaceutical Bulletin·Noriyuki YamaotsuShuichi Hirono
Nov 10, 2013·Bioinformatics·Lydia BenkaidaliMichel Petitjean
Jun 19, 2014·BMC Bioinformatics·Saulo H P OliveiraPaulo S L de Oliveira
Jul 21, 1999·Proceedings of the National Academy of Sciences of the United States of America·I A VakserC F Lam
Jun 28, 2011·Current Opinion in Chemical Biology·Eric B FaumanEnoch S Huang
Jan 17, 2009·Journal of Molecular Graphics & Modelling·P Srivani, G Narahari Sastry
Nov 21, 2007·Journal of Molecular Graphics & Modelling·Donguk KimDeok-Soo Kim
Feb 20, 2007·Journal of Molecular Graphics & Modelling·P SrivaniG Narahari Sastry
Jul 21, 2015·Protein Science : a Publication of the Protein Society·Yingssu TsaiTodd O Yeates
Jan 27, 2011·Chemical Biology & Drug Design·A Srinivas ReddyG Narahari Sastry
Dec 22, 2016·PLoS Computational Biology·Yitav Glantz-GashaiAbraham O Samson
Apr 4, 1997·Journal of Molecular Biology·G JonesR Taylor
Mar 28, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·You-Lu PanJian-Zhong Chen
Jun 1, 2018·International Journal of Molecular Sciences·Philippe UrbanGilles Truan
Aug 2, 2018·Physical Chemistry Chemical Physics : PCCP·Narendra Kumar, Dominik Marx
Mar 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M A Moret, G F Zebende
Oct 15, 2019·PloS One·Sérgio DiasAbel J P Gomes
Mar 10, 2018·Computer Graphics Forum : Journal of the European Association for Computer Graphics·Tiago SimõesAbel Gomes
Nov 19, 2009·Journal of Chemical Information and Modeling·Simone SciabolaJonathan S Mason
Oct 16, 2010·Journal of Chemical Information and Modeling·Andrea VolkamerMatthias Rarey
Feb 23, 2012·Journal of Chemical Information and Modeling·Maria Kontoyianni, Christopher B Rosnick
Jun 24, 2008·Methods : a Companion to Methods in Enzymology·Zheng CaiAlan Berezov

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