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Nucleic Acids Research, 2003, Vol. 31, No. 13 3345-3348
© 2003 Oxford University Press

NCI: a server to identify non-canonical interactions in protein structures

M. Madan Babu*

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK

*To whom correspondence should be addressed. Tel: +44 1223402041; Fax: +44 1223213556; Email: madanm{at}mrc-lmb.cam.ac.uk

NCI is a server for the identification of non-canonical interactions in protein structures. These interactions, which include N-H···{pi}, C{alpha}-H···{pi}, C{alpha}-H···O=C and variants of them, were first observed in small molecules and subsequently in high-resolution protein structures. Such interactions have been subjected to extensive structural analysis to elucidate the different geometric criteria required to identify them. These interactions have also recently been shown to be important for the stability of protein structures. In this work, I describe a server called NCI, which allows the user to either upload protein/peptide coordinates in Protein Data Bank (PDB) format or enter a Structural Classification of Proteins database (SCOP)/PDB identifier for which NCI identifies the different non-canonical interactions, based purely on geometric criteria. Results are presented as an HTML table, as a parseable text file and as a color-coded interaction matrix. In addition, the user can view the RasMol image highlighting the interactions in the protein structure and download the RasMol script. The NCI server is available at: http://www.mrc-lmb.cam.ac.uk/genomes/nci/.


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K. G. Tina, R. Bhadra, and N. Srinivasan
PIC: Protein Interactions Calculator
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W473 - W476.
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