Rapid catalytic template searching as an enzyme function prediction procedure.

We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time a...

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Autores principales:	Jerome P Nilmeier, Daniel A Kirshner, Sergio E Wong, Felice C Lightstone
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e00c6b05f15a48fd8e0da4b0f2f56080
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spelling	oai:doaj.org-article:e00c6b05f15a48fd8e0da4b0f2f560802021-11-18T07:46:08ZRapid catalytic template searching as an enzyme function prediction procedure.1932-620310.1371/journal.pone.0062535https://doaj.org/article/e00c6b05f15a48fd8e0da4b0f2f560802013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23675414/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues--The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches.Jerome P NilmeierDaniel A KirshnerSergio E WongFelice C LightstonePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e62535 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jerome P Nilmeier Daniel A Kirshner Sergio E Wong Felice C Lightstone Rapid catalytic template searching as an enzyme function prediction procedure.
description	We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues--The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches.
format	article
author	Jerome P Nilmeier Daniel A Kirshner Sergio E Wong Felice C Lightstone
author_facet	Jerome P Nilmeier Daniel A Kirshner Sergio E Wong Felice C Lightstone
author_sort	Jerome P Nilmeier
title	Rapid catalytic template searching as an enzyme function prediction procedure.
title_short	Rapid catalytic template searching as an enzyme function prediction procedure.
title_full	Rapid catalytic template searching as an enzyme function prediction procedure.
title_fullStr	Rapid catalytic template searching as an enzyme function prediction procedure.
title_full_unstemmed	Rapid catalytic template searching as an enzyme function prediction procedure.
title_sort	rapid catalytic template searching as an enzyme function prediction procedure.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/e00c6b05f15a48fd8e0da4b0f2f56080
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Rapid catalytic template searching as an enzyme function prediction procedure.

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