Development of unified statistical potentials describing protein-protein interactions. Export

@article{citeulike:139500, abstract = {A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a nonredundant, high-quality dimer database is constructed. The protein complexes in this dataset are checked by a literature search to confirm that they form multimers, and the pairwise amino acid preference to interact across a protein-protein interface is analyzed and pair potentials constructed. The performance of the residue-based potentials is evaluated by using four jackknife tests and by assessing the potentials' ability to select true protein-protein interfaces from false ones. Compared to potentials developed for monomeric protein structure prediction, the interdomain potential performs much better at distinguishing protein-protein interactions. The potential developed from homodimer interfaces is almost the same as that developed from heterodimer interfaces with a correlation coefficient of 0.92. The residue-based potential is well suited for genomic scale protein interaction prediction and analysis, such as in a recently developed threading-based algorithm, MULTIPROSPECTOR. However, the more time-consuming atom-based potential performs better in identifying near-native structures from docking generated decoys.}, address = {Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.}, author = {Lu, H. and Lu, L. and Skolnick, J.}, citeulike-article-id = {139500}, citeulike-linkout-0 = {http://www.biophysj.org/cgi/content/abstract/84/3/1895}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/12609891}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=12609891}, issn = {0006-3495}, journal = {Biophys J}, keywords = {interactions, multiprospector, predictions, statpot, structure}, month = {March}, number = {3}, pages = {1895--1901}, posted-at = {2008-08-15 17:05:08}, priority = {0}, title = {Development of unified statistical potentials describing protein-protein interactions.}, url = {http://www.biophysj.org/cgi/content/abstract/84/3/1895}, volume = {84}, year = {2003} }

TY - JOUR ID - citeulike:139500 L3 - citeulike-article-id:139500 N2 - A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a nonredundant, high-quality dimer database is constructed. The protein complexes in this dataset are checked by a literature search to confirm that they form multimers, and the pairwise amino acid preference to interact across a protein-protein interface is analyzed and pair potentials constructed. The performance of the residue-based potentials is evaluated by using four jackknife tests and by assessing the potentials' ability to select true protein-protein interfaces from false ones. Compared to potentials developed for monomeric protein structure prediction, the interdomain potential performs much better at distinguishing protein-protein interactions. The potential developed from homodimer interfaces is almost the same as that developed from heterodimer interfaces with a correlation coefficient of 0.92. The residue-based potential is well suited for genomic scale protein interaction prediction and analysis, such as in a recently developed threading-based algorithm, MULTIPROSPECTOR. However, the more time-consuming atom-based potential performs better in identifying near-native structures from docking generated decoys. IS - 3 JF - Biophys J SN - 0006-3495 AD - Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA. EP - 1901 TI - Development of unified statistical potentials describing protein-protein interactions. VL - 84 SP - 1895 KW - interactions KW - multiprospector KW - predictions KW - statpot KW - structure AU - Lu, H AU - Lu, L AU - Skolnick, J PY - 2003/03// UR - http://www.biophysj.org/cgi/content/abstract/84/3/1895 ER -