Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

@article{citeulike:2791320, abstract = {BACKGROUND:Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes can reveal the details of their function and provide a basis for many computational and experimental approaches. Differentiation between biological and non-biological contacts and reconstruction of the intact complex is a challenging computational problem. A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB).RESULTS:We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) combining these scores for each PDB entry in order to predict the complex structure. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions. These interfaces, as well as the predicted protein complexes, are available from the Protein Interface Server (PInS) website at http://pins.ornl.gov/.CONCLUSIONS:Our method demonstrates an almost two-fold reduction of the annotation error rate as evaluated on a large benchmark set of complexes validated from the literature. We also estimate relative contributions of each interface property to the accurate discrimination of biologically relevant interfaces and discuss possible directions for further improving the prediction method.}, author = {Bordner, Andrew and Gorin, Andrey }, citeulike-article-id = {2791320}, doi = {10.1186/1471-2105-9-234}, journal = {BMC Bioinformatics}, keywords = {bioinformatics, complex, interaction, interface, pdb, protein-protein}, number = {1}, posted-at = {2008-05-13 00:10:20}, priority = {2}, title = {Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces}, url = {http://dx.doi.org/10.1186/1471-2105-9-234}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2791320 L3 - citeulike-article-id:2791320 TI - Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces JF - BMC Bioinformatics VL - 9 IS - 1 N2 - BACKGROUND:Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes can reveal the details of their function and provide a basis for many computational and experimental approaches. Differentiation between biological and non-biological contacts and reconstruction of the intact complex is a challenging computational problem. A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB).RESULTS:We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) combining these scores for each PDB entry in order to predict the complex structure. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions. These interfaces, as well as the predicted protein complexes, are available from the Protein Interface Server (PInS) website at http://pins.ornl.gov/.CONCLUSIONS:Our method demonstrates an almost two-fold reduction of the annotation error rate as evaluated on a large benchmark set of complexes validated from the literature. We also estimate relative contributions of each interface property to the accurate discrimination of biologically relevant interfaces and discuss possible directions for further improving the prediction method. KW - bioinformatics KW - complex KW - interaction KW - interface KW - pdb KW - protein-protein AU - Bordner, Andrew AU - Gorin, Andrey PY - 2008/// UR - http://dx.doi.org/10.1186/1471-2105-9-234 ER -