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PROMALS3D: a tool for multiple protein sequence and structure alignments

Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structure...

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Detalles Bibliográficos
Autores principales: Pei, Jimin, Kim, Bong-Hyun, Grishin, Nick V.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367709/
https://www.ncbi.nlm.nih.gov/pubmed/18287115
http://dx.doi.org/10.1093/nar/gkn072
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author Pei, Jimin
Kim, Bong-Hyun
Grishin, Nick V.
author_facet Pei, Jimin
Kim, Bong-Hyun
Grishin, Nick V.
author_sort Pei, Jimin
collection PubMed
description Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural information to guide sequence alignments constructed by our MSA program PROMALS. The resulting tool, PROMALS3D, automatically identifies homologs with known 3D structures for the input sequences, derives structural constraints through structure-based alignments and combines them with sequence constraints to construct consistency-based multiple sequence alignments. The output is a consensus alignment that brings together sequence and structural information about input proteins and their homologs. PROMALS3D can also align sequences of multiple input structures, with the output representing a multiple structure-based alignment refined in combination with sequence constraints. The advantage of PROMALS3D is that it gives researchers an easy way to produce high-quality alignments consistent with both sequences and structures of proteins. PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods.
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spelling pubmed-23677092008-05-07 PROMALS3D: a tool for multiple protein sequence and structure alignments Pei, Jimin Kim, Bong-Hyun Grishin, Nick V. Nucleic Acids Res Computational Biology Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural information to guide sequence alignments constructed by our MSA program PROMALS. The resulting tool, PROMALS3D, automatically identifies homologs with known 3D structures for the input sequences, derives structural constraints through structure-based alignments and combines them with sequence constraints to construct consistency-based multiple sequence alignments. The output is a consensus alignment that brings together sequence and structural information about input proteins and their homologs. PROMALS3D can also align sequences of multiple input structures, with the output representing a multiple structure-based alignment refined in combination with sequence constraints. The advantage of PROMALS3D is that it gives researchers an easy way to produce high-quality alignments consistent with both sequences and structures of proteins. PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods. Oxford University Press 2008-04 2008-02-20 /pmc/articles/PMC2367709/ /pubmed/18287115 http://dx.doi.org/10.1093/nar/gkn072 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Pei, Jimin
Kim, Bong-Hyun
Grishin, Nick V.
PROMALS3D: a tool for multiple protein sequence and structure alignments
title PROMALS3D: a tool for multiple protein sequence and structure alignments
title_full PROMALS3D: a tool for multiple protein sequence and structure alignments
title_fullStr PROMALS3D: a tool for multiple protein sequence and structure alignments
title_full_unstemmed PROMALS3D: a tool for multiple protein sequence and structure alignments
title_short PROMALS3D: a tool for multiple protein sequence and structure alignments
title_sort promals3d: a tool for multiple protein sequence and structure alignments
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367709/
https://www.ncbi.nlm.nih.gov/pubmed/18287115
http://dx.doi.org/10.1093/nar/gkn072
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