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Title: Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach
Author: Núñez Vivanco, Gabriel
Valdés Jiménez, Alejandro
Besoaín Pino, Felipe Andrés
Reyes Parada, Miguel
Others: Universidad de Talca
Universidad de Santiago de Chile
Universitat Oberta de Catalunya. Internet Interdisciplinary Institute (IN3)
Keywords: pattern
Issue Date: 18-Apr-2016
Publisher: Journal of Cheminformatics
Citation: Núñez-Vivanco, G., Valdés-Jiménez, A., Besoaín, F. & Reyes-Parada, M. (2016). Geomfinder: A multi-feature identifier of similar three-dimensional protein patterns: A ligand-independent approach. Journal of Cheminformatics, 8(1). doi: 10.1186/s13321-016-0131-9
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Abstract: Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, protein clustering, drug discovery and the establishment of evolutionary relationships. Thus, several computational applications to identify, describe and compare 3D patterns (or motifs) have been developed. Often, these tools consider a 3D pattern as that described by the residues surrounding co-crystallized/docked ligands available from X-ray crystal structures or homology models. Nevertheless, many of the protein structures stored in public databases do not provide information about the location and characteristics of ligand binding sites and/or other important 3D patterns such as allosteric sites, enzyme-cofactor interaction motifs, etc. This makes necessary the development of new ligand-independent methods to search and compare 3D patterns in all available protein structures.
Language: English
ISSN: 1758-2946MIAR
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