An integrated system for studying residue coevolution in proteins Export

@article{citeulike:2230285, abstract = {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 10.1093/bioinformatics/btm584}, author = {Yip, Kevin Y. and Patel, Prianka and Kim, Philip M. and Engelman, Donald M. and Mcdermott, Drew and Gerstein, Mark}, citeulike-article-id = {2230285}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btm584}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/2/290}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18056067}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18056067}, day = {15}, doi = {10.1093/bioinformatics/btm584}, journal = {Bioinformatics}, keywords = {coevolution, evo\_502}, month = {January}, number = {2}, pages = {290--292}, posted-at = {2008-03-26 12:42:11}, priority = {0}, title = {An integrated system for studying residue coevolution in proteins}, url = {http://dx.doi.org/10.1093/bioinformatics/btm584}, volume = {24}, year = {2008} }

TY - JOUR ID - citeulike:2230285 L3 - citeulike-article-id:2230285 N2 - 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 10.1093/bioinformatics/btm584 IS - 2 JF - Bioinformatics EP - 292 TI - An integrated system for studying residue coevolution in proteins VL - 24 SP - 290 KW - coevolution KW - evo_502 AU - Yip, Kevin AU - Patel, Prianka AU - Kim, Philip AU - Engelman, Donald AU - Mcdermott, Drew AU - Gerstein, Mark PY - 2008/01/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btm584 ER -