An integrated system for studying residue coevolution in proteins

Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not much is known about their relative strengths and weaknesses. Also, subtle algorithmic details have di...

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Bibliographic Details
Published in:Bioinformatics 2008-01, Vol.24 (2), p.290-292
Main Authors: Yip, Kevin Y., Patel, Prianka, Kim, Philip M., Engelman, Donald M., McDermott, Drew, Gerstein, Mark
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Biological and medical sciences
Computer Graphics
Evolution, Molecular
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Molecular Sequence Data
Protein Conformation
Proteins - chemistry
Proteins - genetics
Proteins - ultrastructure
Sequence Analysis, Protein - methods
Software
Systems Integration
User-Computer Interface
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Summary:Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not much is known about their relative strengths and weaknesses. Also, subtle algorithmic details have discouraged implementing and comparing them. We addressed this issue by developing an integrated online system that enables comparative analyses with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods. A set of data preprocessing options are provided for improving the sensitivity and specificity of coevolution signal detection, including sequence weighting, residue grouping and the filtering of sequences, sites and site pairs. A total of more than 100 scoring variations are available. The system also provides facilities for studying the relationship between coevolution scores and inter-residue distances from a crystal structure if provided, which may help in understanding protein structures. Availability: The system is available at http://coevolution.gersteinlab.org. The source code and JavaDoc API can also be downloaded from the web site. Contact: mark.gerstein@yale.edu Supplementary information: Additional materials can be found at http://coevolution.gersteinlab.org/coevolution/supp.jsp
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btm584