OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. Export

@article{citeulike:2578293, abstract = {Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interactions among main-chain atoms, its success highlights the crucial importance of side-chain packing in forming native protein structures. Moreover, OPUS-PSP does not explicitly include solvation terms, and thus the potential should perform well when the solvation effect is difficult to determine, such as in membrane proteins. Overall, OPUS-PSP is a generally applicable potential for protein structure modeling, especially for handling side-chain conformations, one of the most difficult steps in high-accuracy protein structure prediction and refinement.}, author = {Lu, Mingyang and Dousis, Athanasios D. and Ma, Jianpeng}, citeulike-article-id = {2578293}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jmb.2007.11.033}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18177896}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18177896}, citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6WK7-4R5HNNC-2/2/3017c149336a061eefc904074343369d}, day = {8}, doi = {10.1016/j.jmb.2007.11.033}, issn = {1089-8638}, journal = {Journal of molecular biology}, keywords = {energy, function}, month = {February}, number = {1}, pages = {288--301}, posted-at = {2008-03-24 04:37:40}, priority = {2}, title = {OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.}, url = {http://dx.doi.org/10.1016/j.jmb.2007.11.033}, volume = {376}, year = {2008} }

TY - JOUR ID - citeulike:2578293 L3 - citeulike-article-id:2578293 N2 - Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interactions among main-chain atoms, its success highlights the crucial importance of side-chain packing in forming native protein structures. Moreover, OPUS-PSP does not explicitly include solvation terms, and thus the potential should perform well when the solvation effect is difficult to determine, such as in membrane proteins. Overall, OPUS-PSP is a generally applicable potential for protein structure modeling, especially for handling side-chain conformations, one of the most difficult steps in high-accuracy protein structure prediction and refinement. IS - 1 JF - Journal of molecular biology SN - 1089-8638 EP - 301 TI - OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. VL - 376 SP - 288 KW - energy KW - function AU - Lu, Mingyang AU - Dousis, Athanasios AU - Ma, Jianpeng PY - 2008/02/08/ UR - http://dx.doi.org/10.1016/j.jmb.2007.11.033 ER -