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

Content Provider	Springer Nature Link
Author	Koczyk, Grzegorz Wyrwicz, Lucjan S. Rychlewski, Leszek
Copyright Year	2007
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. Figure Information flow in LigProf database construction pipeline
Starting Page	445
Ending Page	455
Page Count	11
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	13
Issue Number	3
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2007-01-03
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Ligand-binding sites Profiles Structural genomics Computer Application in Life Sciences Life Sciences Health Informatics Molecular Medicine Biomedicine general Computer Applications in Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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