Cargando…

Estimation of protein function using template-based alignment of enzyme active sites

BACKGROUND: The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection...

Descripción completa

Detalles Bibliográficos
Autores principales: Hanson, Brett, Westin, Charles, Rosa, Mario, Grier, Alexander, Osipovitch, Mikhail, MacDonald, Madolyn L, Dodge, Greg, Boli, Paule M, Corwin, Cyprian W, Kessler, Haeja, McKay, Talia, Bernstein, Herbert J, Craig, Paul A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229977/
https://www.ncbi.nlm.nih.gov/pubmed/24669788
http://dx.doi.org/10.1186/1471-2105-15-87
_version_ 1782344202857742336
author Hanson, Brett
Westin, Charles
Rosa, Mario
Grier, Alexander
Osipovitch, Mikhail
MacDonald, Madolyn L
Dodge, Greg
Boli, Paule M
Corwin, Cyprian W
Kessler, Haeja
McKay, Talia
Bernstein, Herbert J
Craig, Paul A
author_facet Hanson, Brett
Westin, Charles
Rosa, Mario
Grier, Alexander
Osipovitch, Mikhail
MacDonald, Madolyn L
Dodge, Greg
Boli, Paule M
Corwin, Cyprian W
Kessler, Haeja
McKay, Talia
Bernstein, Herbert J
Craig, Paul A
author_sort Hanson, Brett
collection PubMed
description BACKGROUND: The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function. Functional residues are critical components of predictively useful motifs. We have implemented a novel method, to complement current approaches, which detects motifs solely on the basis of distance restraints between catalytic residues. RESULTS: ProMOL is a plugin for the PyMOL molecular graphics environment that can be used to create active site motifs for enzymes. A library of 181 active site motifs has been created with ProMOL, based on definitions published in the Catalytic Site Atlas (CSA). Searches with ProMOL produce better than 50% useful Enzyme Commission (EC) class suggestions for level 1 searches in EC classes 1, 4 and 5, and produce some useful results for other classes. 261 additional motifs automatically translated from Jonathan Barker’s JESS motif set [Bioinformatics 19:1644–1649, 2003] and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search methods. CONCLUSION: The ProMOL plugin for PyMOL provides ready access to template-based local alignments. Recent improvements to ProMOL, including the expanded motif library, RMSD calculations and output selection formatting, have greatly increased the program’s usability and speed, and have improved the way that the results are presented.
format Online
Article
Text
id pubmed-4229977
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-42299772014-11-14 Estimation of protein function using template-based alignment of enzyme active sites Hanson, Brett Westin, Charles Rosa, Mario Grier, Alexander Osipovitch, Mikhail MacDonald, Madolyn L Dodge, Greg Boli, Paule M Corwin, Cyprian W Kessler, Haeja McKay, Talia Bernstein, Herbert J Craig, Paul A BMC Bioinformatics Software BACKGROUND: The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function. Functional residues are critical components of predictively useful motifs. We have implemented a novel method, to complement current approaches, which detects motifs solely on the basis of distance restraints between catalytic residues. RESULTS: ProMOL is a plugin for the PyMOL molecular graphics environment that can be used to create active site motifs for enzymes. A library of 181 active site motifs has been created with ProMOL, based on definitions published in the Catalytic Site Atlas (CSA). Searches with ProMOL produce better than 50% useful Enzyme Commission (EC) class suggestions for level 1 searches in EC classes 1, 4 and 5, and produce some useful results for other classes. 261 additional motifs automatically translated from Jonathan Barker’s JESS motif set [Bioinformatics 19:1644–1649, 2003] and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search methods. CONCLUSION: The ProMOL plugin for PyMOL provides ready access to template-based local alignments. Recent improvements to ProMOL, including the expanded motif library, RMSD calculations and output selection formatting, have greatly increased the program’s usability and speed, and have improved the way that the results are presented. BioMed Central 2014-03-27 /pmc/articles/PMC4229977/ /pubmed/24669788 http://dx.doi.org/10.1186/1471-2105-15-87 Text en Copyright © 2014 Hanson et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Software
Hanson, Brett
Westin, Charles
Rosa, Mario
Grier, Alexander
Osipovitch, Mikhail
MacDonald, Madolyn L
Dodge, Greg
Boli, Paule M
Corwin, Cyprian W
Kessler, Haeja
McKay, Talia
Bernstein, Herbert J
Craig, Paul A
Estimation of protein function using template-based alignment of enzyme active sites
title Estimation of protein function using template-based alignment of enzyme active sites
title_full Estimation of protein function using template-based alignment of enzyme active sites
title_fullStr Estimation of protein function using template-based alignment of enzyme active sites
title_full_unstemmed Estimation of protein function using template-based alignment of enzyme active sites
title_short Estimation of protein function using template-based alignment of enzyme active sites
title_sort estimation of protein function using template-based alignment of enzyme active sites
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229977/
https://www.ncbi.nlm.nih.gov/pubmed/24669788
http://dx.doi.org/10.1186/1471-2105-15-87
work_keys_str_mv AT hansonbrett estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT westincharles estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT rosamario estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT grieralexander estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT osipovitchmikhail estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT macdonaldmadolynl estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT dodgegreg estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT bolipaulem estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT corwincyprianw estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT kesslerhaeja estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT mckaytalia estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT bernsteinherbertj estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites
AT craigpaula estimationofproteinfunctionusingtemplatebasedalignmentofenzymeactivesites