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Nucleic Acids Research 2005 33(Web Server Issue):W39-W43; doi:10.1093/nar/gki398
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment

Vladimir Sobolev*, Eran Eyal, Sergey Gerzon, Vladimir Potapov, Mariana Babor, Jaime Prilusky1 and Marvin Edelman

Department of Plant Sciences, Weizmann Institute of Science Rehovot 76100, Israel 1Department of Biological Services, Weizmann Institute of Science Rehovot 76100, Israel

*To whom correspondence should be addressed. Tel: +972 8 9344434; Fax: +972 8 9469124; Email: vladimir.sobolev{at}weizmann.ac.il

Received February 13, 2005. Revised March 14, 2005. Accepted March 14, 2005.

We describe a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes. LPC/CSU software provides a common definition of inter-atomic contacts and complementarity of contacting surfaces to analyze protein structure and complexes. In the current version of LPC/CSU, analyses of water molecules and nucleic acids have been added, together with improved and expanded visualization options using Chime or Java based Jmol. The SPACE suite includes servers and programs for: structural analysis of point mutations (MutaProt); side chain modeling based on surface complementarity (SCCOMP); building a crystal environment and analysis of crystal contacts (CryCo); construction and analysis of protein contact maps (CMA) and molecular docking software (LIGIN). The SPACE suite is accessed at http://ligin.weizmann.ac.il/space.


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