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Nucleic Acids Research 2005 33(Web Server Issue):W50-W55; doi:10.1093/nar/gki416
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology

Alessandro Paiardini, Francesco Bossa and Stefano Pascarella1,*

Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’, Università La Sapienza Piazzale Aldo Moro 5, 00185 Roma, Italy 1Centro Interdipartimentale di Ricerca per la Analisi dei Modelli e dell'Informazione nei Sistemi Biomedici (CISB), Università La Sapienza Piazzale Aldo Moro 5, 00185 Roma, Italy

*To whom correspondence should be addressed. Tel: +39 06 49917574; Fax: +39 06 49917566; Email: stefano.pascarella{at}uniroma1.it

Received February 8, 2005. Revised March 21, 2005. Accepted March 21, 2005.

The identification of evolutionarily conserved features of protein structures can provide insights into their functional and structural properties. Three methods have been developed and implemented as WWW tools, CAMPO, SCR_FIND and CHC_FIND, to analyze evolutionarily conserved residues (ECRs), structurally conserved regions (SCRs) and conserved hydrophobic contacts (CHCs) in protein families and superfamilies, on the basis of their 3D structures and the homologous sequences available. The programs identify protein segments that conserve a similar main-chain conformation, compute residue-to-residue hydrophobic contacts involving only apolar atoms common to all the 3D structures analyzed and allow the identification of conserved amino-acid sites among protein structures and their homologous sequences. The programs also allow the visualization of SCRs, CHCs and ECRs directly on the superposed structures and their multiple structural and sequence alignments. Tools and tutorials explaining their usage are available at http://schubert.bio.uniroma1.it/SCR_FIND, http://schubert.bio.uniroma1.it/CHC_FIND and http://schubert.bio.uniroma1.it/CAMPO.


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[Abstract] [Full Text] [PDF]


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