OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

@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}, doi = {http://dx.doi.org/10.1016/j.jmb.2007.11.033}, 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 TI - OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing JF - Journal of Molecular Biology VL - 376 IS - 1 SP - 288 EP - 301 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. 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 -