[duplicate] Local Function Conservation in Sequence and Structure Space

by: Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer

PLoS Comput Biol, Vol. 4, No. 7. (4 July 2008), e1000105.

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Abstract

We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de).

@article{citeulike:2971087, abstract = {We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de).}, author = {Weinhold, Nils and Sander, Oliver and Domingues, Francisco S. and Lengauer, Thomas and Sommer, Ingolf }, citeulike-article-id = {2971087}, doi = {http://dx.doi.org/10.1371/journal.pcbi.1000105}, journal = {PLoS Comput Biol}, month = {July}, number = {7}, pages = {e1000105+}, posted-at = {2008-07-07 23:26:46}, priority = {2}, publisher = {Public Library of Science}, title = {[duplicate] Local Function Conservation in Sequence and Structure Space}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000105}, volume = {4}, year = {2008} }

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TY - JOUR ID - citeulike:2971087 L3 - citeulike-article-id:2971087 TI - [duplicate] Local Function Conservation in Sequence and Structure Space JF - PLoS Comput Biol VL - 4 IS - 7 SP - e1000105 PB - Public Library of Science N2 - We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de). AU - Weinhold, Nils AU - Sander, Oliver AU - Domingues, Francisco AU - Lengauer, Thomas AU - Sommer, Ingolf PY - 2008/07/04/ UR - http://dx.doi.org/10.1371/journal.pcbi.1000105 ER -

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