OPUS-PSP : Orientation-dependent statistical all-atom potential derived from side-chain packing

OPUS-PSP 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. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials. OPUS-PSP is applicable to protein structure modelling, especially for handling side-chain conformations. Linux x86 version is freely available to academic users.

Reference : OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing. Mingyang Lu, Athanasios D.Dousis and Jianpeng Ma, JMB (2008) 376, 288-301

OPUS-Ca : Knowledge-based potential function requiring only C-alpha positions

The OPUS-Ca potential requires only C-alpha positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a C-alpha trace for auxiliary purposes. The potential function is formed based on seven major representative molecular interactions in proteins: distance-dependent pairwise energy with orientational preference, hydrogen bonding energy, short-range energy, packing energy, tri-peptide packing energy, three-body energy, and solvation energy. From the testing of decoy recognition on a number of commonly used decoy sets, it is shown that the new potential function outperforms all known C-alpha-based potentials and most other coarse-grained ones that require more information than C-alpha positions. Linux x86 version is freely available to academic users.

Reference : OPUS-Ca: A Knowledge-based Potential Function Requiring only C-alpha Positions. Yinghao Wu, Mingyang Lu, Mingzhi Chen, Jialin Li, and Jianpeng Ma, Protein Sci. (2007) 16, 1449-1463.

OPUS-Rota : Side-chain modeling method

OPUS-Rota integrates our recently published all-atom statistical potential OPUS-PSP, and a pair-wise solvation energy term. OPUS-Rota is more accurate than SCWRL with similar excution speed, and it has accuracy comparable to or better than the most accurate methods in the literature, but with one or two-orders-of-magnitude-shorter run time. Linux x86 version is freely available to academic users.

Reference : OPUS-Rota: A Fast and Accurate Method for Side-chain Modeling. Mingyang Lu, Athanasios D.Dousis and Jianpeng Ma, Protein Science (2008) 17, 1576-1585