An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction Export

@article{RAPDF, abstract = {We present a formalism to compute the probability of an amino acid sequence conformation being native-like, given a set of pairwise atom-atom distances. The formalism is used to derive three discriminatory functions with different types of representations for the atom-atom contacts observed in a database of protein structures. These functions include two virtual atom representations and one all-heavy atom representation. When applied to six different decoy sets containing a range of correct and incorrect conformations of amino acid sequences, the all-atom distance-dependent discriminatory function is able to identify correct from incorrect more often than the discriminatory functions using approximate representations. We illustrate the importance of using a detailed atomic description for obtaining the most accurate discrimination, and the necessity for testing discriminatory functions against a wide variety of decoys. The discriminatory function is also shown to be capable of capturing the fine details of atom-atom preferences. These results suggest that the all-atom distance-dependent discriminatory function will be useful for protein structure prediction and model refinement.}, author = {Samudrala, Ram and Moult, John}, citeulike-article-id = {2224252}, citeulike-linkout-0 = {http://dx.doi.org/10.1006/jmbi.1997.1479}, citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6WK7-45P0FFJ-1F/2/92478c2c01ea76ac51435bdda6846bfe}, day = {6}, doi = {10.1006/jmbi.1997.1479}, journal = {Journal of Molecular Biology}, keywords = {energy, function}, month = {February}, number = {5}, pages = {895--916}, posted-at = {2008-01-13 04:13:02}, priority = {2}, title = {An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction}, url = {http://dx.doi.org/10.1006/jmbi.1997.1479}, volume = {275}, year = {1998} }

TY - JOUR ID - RAPDF L3 - citeulike-article-id:2224252 N2 - We present a formalism to compute the probability of an amino acid sequence conformation being native-like, given a set of pairwise atom-atom distances. The formalism is used to derive three discriminatory functions with different types of representations for the atom-atom contacts observed in a database of protein structures. These functions include two virtual atom representations and one all-heavy atom representation. When applied to six different decoy sets containing a range of correct and incorrect conformations of amino acid sequences, the all-atom distance-dependent discriminatory function is able to identify correct from incorrect more often than the discriminatory functions using approximate representations. We illustrate the importance of using a detailed atomic description for obtaining the most accurate discrimination, and the necessity for testing discriminatory functions against a wide variety of decoys. The discriminatory function is also shown to be capable of capturing the fine details of atom-atom preferences. These results suggest that the all-atom distance-dependent discriminatory function will be useful for protein structure prediction and model refinement. IS - 5 JF - Journal of Molecular Biology EP - 916 TI - An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction VL - 275 SP - 895 KW - energy KW - function AU - Samudrala, Ram AU - Moult, John PY - 1998/02/06/ UR - http://dx.doi.org/10.1006/jmbi.1997.1479 ER -