: Normal-mode-based thermal parameter X-ray refinement
OPUS-XREF contains two modules: ENMCALC and REFMAC-NM ENMCALC is C -based Elastic Network Model in internal coordinates, specifically designed to eliminate "tip effects" in the normal modes. In OPUS-XREF, ENMCALC is used to calculate the normal modes of a protein structure for REFMAC-NM. REFMAC-NM constructs anisotropic temperature factors based on normal mode vectors and optimizes the contribution of each normal mode. It is based on REFMAC 5.2 developed by Garib Murshudov and co-workers, modified by Mingyang Lu and Athanasios D. Dousis (Nov 2008) Linux x86 version is freely available to academic users.
Reference : Xiaorui Chen, Billy K. Poon, Athanasios Dousis, Qinghua Wang & Jianpeng Ma "Normal Mode Refinement of Anisotropic Thermal Parameters for Potassium Channel KcsA at 3.2-A Crystallographic Resolution." Structure 15 :955-962. (2007); Poon BK, Chen X, Lu M, Vyas NK, Quiocho FA, Wang Q, Ma J. "Normal Mode Refinement of Anisotropic Thermal Parameters for a Supramolecular Complex at 3.42-A Crystallographic Resolution." PNAS, 104, 7869-7874. (2007); Lu M, Poon B, Ma J. "A New Method for Coarse-Grained Elastic Normal-Mode Analysis." J. Chem. Theory and Comput, 2(3), 464-471. (2006) Chen X, Poon BK, Dousis AD, Wang Q, Ma J.
: 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
: 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.
: 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
Enhanced sampling for folding proteins in explicit solvent
Download source code and a modification for helical proteins.
It requires GROMACS 4.0.7,
AMBER force field ffamber
(and a modification ffamber*).
Reference: Enhanced sampling and applications in protein folding in explicit solvent.
Cheng Zhang and Jianpeng Ma,
J. Chem. Phys. (2010) 132 244101
Parallel Continuous Simulated Tempering (PCST) method
Download the modified GROMACS 4.6.3 with PCST implemented.
Reference: Parallel continuous simulated tempering and its applications in large-scale molecular simulations.
Tianwu Zang, Linglin Yu, Chong Zhang and Jianpeng Ma,
J. Chem. Phys. (2014) 141 044113
: Distance- and Orientation-Dependent All-AtomPotential Derived from Side-Chain Packing
OPUS-DOSP considers distance or orientation contribution depending on the range of contact distance and adds a new auxiliary function in energy function in addition to the traditional Boltzmann term, in order to adjust the contributions of extreme cases.The basic framework is based on OPUS-PSP.
Reference: OPUS-DOSP:A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing. Gang Xu, Tianqi Ma, Tianwu Zang, Weitao Sun, Qinghua Wang and Jianpeng Ma, JMB (2017) 429, 3113-3120
: C-atom-based scoring function for ranking protein structural models
OPUS-CSF built a scoring function (CSF score) based on the native distributions (derived from the entire PDB) of coordinate components of mainchain C (carbonyl) atoms on selected residues of peptide segments of 5, 7, 9, and 11 residues in length rather than using traditional Boltzmann formula.
Reference: OPUS-DOSP:A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing. Gang Xu, Tianqi Ma, Tianwu Zang, Weitao Sun, Qinghua Wang and Jianpeng Ma, Protein Science (2018) 27(1), 286-292