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LigProf: A simple tool for in silico prediction of ligand-binding sites

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Abstract

With the increasing amount of data provided by both high-throughput sequencing and structural genomics studies, there is a growing need for tools to augment functional predictions for protein sequences. Broad descriptions of function can be provided by establishing the presence of protein domains associated with a particular function. To extend the domain-based annotation, LigProf provides predictions of potential ligands that bind to a protein, as well as critical residues that stabilize ligands. A P-value statistic for estimating the significance of motif occurrence is provided for all sites. Although the usefulness of the method will rise with increasing numbers of crystallographically solved molecules deposited in the PDB database, we show that it can already be applied successfully to the highly represented ligand-bound protein kinase domains of viral and human origin. The LigProf webserver is freely available at: http://www.cropnet.pl/ligprof. At present, LigProf descriptors annotate and extend major protein families from the PfamA database.

Information flow in LigProf database construction pipeline

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Acknowledgements

This work has been supported by grants from the following EU projects: DATAGENOM (LSHB-CT-2003-503017) and GENEFUN (LSHG-CT-2004-503567). LSW was supported by a Program for Young Researchers from the Foundation of Polish Science and MNiSW research grants (2 P05A 001 30, PBZ-MNiI-2/1/2005).

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Authors and Affiliations

  1. Institute of Plant Genetics, Strzeszyńska 34, 60-479, Poznań, Poland

    Grzegorz Koczyk

  2. BioInfoBank Institute, Limanowskiego 24A, 60-744, Poznań, Poland

    Grzegorz Koczyk, Lucjan S. Wyrwicz & Leszek Rychlewski

  3. Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland

    Lucjan S. Wyrwicz

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  1. Grzegorz Koczyk
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  2. Lucjan S. Wyrwicz
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  3. Leszek Rychlewski
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Correspondence to Grzegorz Koczyk.

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Koczyk, G., Wyrwicz, L.S. & Rychlewski, L. LigProf: A simple tool for in silico prediction of ligand-binding sites. J Mol Model 13, 445–455 (2007). https://doi.org/10.1007/s00894-006-0165-4

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  • DOI: https://doi.org/10.1007/s00894-006-0165-4

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