PROCAIN: Protein profile comparison with assisting information

Yong Wang, Ruslan I. Sadreyev, Nick V. Grishin

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Detection of remote sequence homology is essential for the accurate inference of protein structure, function and evolution. The most sensitive detection methods involve the comparison of evolutionary patterns reflected in multiple sequence alignments (MSAs) of protein families. We present PROCAIN, a new method for MSA comparison based on the combination of 'vertical' MSA context (substitution constraints at individual sequence positions) and 'horizontal' context (patterns of residue content at multiple positions). Based on a simple and tractable profile methodology and primitive measures for the similarity of horizontal MSA patterns, the method achieves the quality of homology detection comparable to a more complex advanced method employing hidden Markov models (HMMs) and secondary structure (SS) prediction. Adding SS information further improves PROCAIN performance beyond the capabilities of current state-of-the-art tools. The potential value of the method for structure/function predictions is illustrated by the detection of subtle homology between evolutionary distant yet structurally similar protein domains. ProCAIn, relevant databases and tools can be downloaded from: http://prodata.swmed.edu/procain/download. The web server can be accessed at http://prodata.swmed.edu/procain/procain.php.

Original languageEnglish (US)
Pages (from-to)3522-3530
Number of pages9
JournalNucleic Acids Research
Volume37
Issue number11
DOIs
StatePublished - 2009

Fingerprint

Sequence Alignment
Proteins
Sequence Homology
Databases

ASJC Scopus subject areas

  • Genetics

Cite this

PROCAIN : Protein profile comparison with assisting information. / Wang, Yong; Sadreyev, Ruslan I.; Grishin, Nick V.

In: Nucleic Acids Research, Vol. 37, No. 11, 2009, p. 3522-3530.

Research output: Contribution to journalArticle

Wang, Yong ; Sadreyev, Ruslan I. ; Grishin, Nick V. / PROCAIN : Protein profile comparison with assisting information. In: Nucleic Acids Research. 2009 ; Vol. 37, No. 11. pp. 3522-3530.
@article{058fd89704974601a346cae9594aa612,
title = "PROCAIN: Protein profile comparison with assisting information",
abstract = "Detection of remote sequence homology is essential for the accurate inference of protein structure, function and evolution. The most sensitive detection methods involve the comparison of evolutionary patterns reflected in multiple sequence alignments (MSAs) of protein families. We present PROCAIN, a new method for MSA comparison based on the combination of 'vertical' MSA context (substitution constraints at individual sequence positions) and 'horizontal' context (patterns of residue content at multiple positions). Based on a simple and tractable profile methodology and primitive measures for the similarity of horizontal MSA patterns, the method achieves the quality of homology detection comparable to a more complex advanced method employing hidden Markov models (HMMs) and secondary structure (SS) prediction. Adding SS information further improves PROCAIN performance beyond the capabilities of current state-of-the-art tools. The potential value of the method for structure/function predictions is illustrated by the detection of subtle homology between evolutionary distant yet structurally similar protein domains. ProCAIn, relevant databases and tools can be downloaded from: http://prodata.swmed.edu/procain/download. The web server can be accessed at http://prodata.swmed.edu/procain/procain.php.",
author = "Yong Wang and Sadreyev, {Ruslan I.} and Grishin, {Nick V.}",
year = "2009",
doi = "10.1093/nar/gkp212",
language = "English (US)",
volume = "37",
pages = "3522--3530",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "11",

}

TY - JOUR

T1 - PROCAIN

T2 - Protein profile comparison with assisting information

AU - Wang, Yong

AU - Sadreyev, Ruslan I.

AU - Grishin, Nick V.

PY - 2009

Y1 - 2009

N2 - Detection of remote sequence homology is essential for the accurate inference of protein structure, function and evolution. The most sensitive detection methods involve the comparison of evolutionary patterns reflected in multiple sequence alignments (MSAs) of protein families. We present PROCAIN, a new method for MSA comparison based on the combination of 'vertical' MSA context (substitution constraints at individual sequence positions) and 'horizontal' context (patterns of residue content at multiple positions). Based on a simple and tractable profile methodology and primitive measures for the similarity of horizontal MSA patterns, the method achieves the quality of homology detection comparable to a more complex advanced method employing hidden Markov models (HMMs) and secondary structure (SS) prediction. Adding SS information further improves PROCAIN performance beyond the capabilities of current state-of-the-art tools. The potential value of the method for structure/function predictions is illustrated by the detection of subtle homology between evolutionary distant yet structurally similar protein domains. ProCAIn, relevant databases and tools can be downloaded from: http://prodata.swmed.edu/procain/download. The web server can be accessed at http://prodata.swmed.edu/procain/procain.php.

AB - Detection of remote sequence homology is essential for the accurate inference of protein structure, function and evolution. The most sensitive detection methods involve the comparison of evolutionary patterns reflected in multiple sequence alignments (MSAs) of protein families. We present PROCAIN, a new method for MSA comparison based on the combination of 'vertical' MSA context (substitution constraints at individual sequence positions) and 'horizontal' context (patterns of residue content at multiple positions). Based on a simple and tractable profile methodology and primitive measures for the similarity of horizontal MSA patterns, the method achieves the quality of homology detection comparable to a more complex advanced method employing hidden Markov models (HMMs) and secondary structure (SS) prediction. Adding SS information further improves PROCAIN performance beyond the capabilities of current state-of-the-art tools. The potential value of the method for structure/function predictions is illustrated by the detection of subtle homology between evolutionary distant yet structurally similar protein domains. ProCAIn, relevant databases and tools can be downloaded from: http://prodata.swmed.edu/procain/download. The web server can be accessed at http://prodata.swmed.edu/procain/procain.php.

UR - http://www.scopus.com/inward/record.url?scp=67649850988&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67649850988&partnerID=8YFLogxK

U2 - 10.1093/nar/gkp212

DO - 10.1093/nar/gkp212

M3 - Article

C2 - 19357092

AN - SCOPUS:67649850988

VL - 37

SP - 3522

EP - 3530

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 11

ER -