GROMACS 4.5: Bộ công cụ mô phỏng phân tử mã nguồn mở có hiệu suất cao và đa luồng
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Bennett, 1976, Efficient estimation of free energy differences from Monte Carlo data, J. Comp. Phys., 22, 245, 10.1016/0021-9991(76)90078-4
Berendsen, 1976, Report of CECAM workshop: models for protein dynamics, Technical report
Bowers, 2006, Scalable algorithms for molecular dynamics simulations on commodity clusters, Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), 10.1109/SC.2006.54
Bowman, 2011, Atomistic folding simulations of the five helix bundle protein 6-85, J. Am. Chem. Soc., 133, 664, 10.1021/ja106936n
Boyce, 2009, Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site, J. Mol. Biol., 394, 747, 10.1016/j.jmb.2009.09.049
Brooks, 2009, Charmm: The biomolecular simulation program, J. Comp. Chem., 30, 1545, 10.1002/jcc.21287
Caleman, 2012, Force field benchmark of organic liquids: density, enthalpy of vaporization, heat capacities, surface tension, compressibility, expansion coefficient and dielectric constant, J. Chem. Theor. Comput., 8, 61, 10.1021/ct200731v
Chong, 1999, Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48g7, Proc. Natl Acad. Sci. USA, 96, 14330, 10.1073/pnas.96.25.14330
Christen, 2005, The gromos software for biomolecular simulation: Gromos05, J. Comp. Chem., 26, 1719, 10.1002/jcc.20303
Duan, 1998, Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution, Science, 282, 740, 10.1126/science.282.5389.740
Hawkins, 1996, Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium, J. Phys. Chem. A, 100, 19824, 10.1021/jp961710n
Helms, 1998, Computational alchemy to calculate absolute protein-ligand binding free energy, J. Am. Chem. Soc., 120, 2710, 10.1021/ja9738539
Hess, 2008, Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theor. Comput., 4, 435, 10.1021/ct700301q
Huang, 2011, The free energy landscape of small molecule unbinding, PLoS Comput. Biol., 7, e1002002, 10.1371/journal.pcbi.1002002
Hub, 2010, g_wham-a free weighted histogram analysis implementation including robust error and autocorrelation estimates, J. Chem. Theor. Comput., 6, 3713, 10.1021/ct100494z
Humphrey, 1996, VMD—Visual Molecular Dynamics, J. Molec. Graphics, 14, 33, 10.1016/0263-7855(96)00018-5
Kasson, 2010, Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails, PLoS Comput. Biol., 6, e1000829, 10.1371/journal.pcbi.1000829
Lange, 2010, Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data, Biophys. J., 99, 647, 10.1016/j.bpj.2010.04.062
Larsson, 2012, Virus capsid dissolution studied by microsecond molecular dynamics simulations, PLoS Comput. Biol., 8, e1002502, 10.1371/journal.pcbi.1002502
Larsson, 2010, A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling, J. Comp. Chem., 31, 2593, 10.1002/jcc.21552
Levitt, 1969, Refinement of protein conformations using a macromolecular energy minimization procedure, J. Mol. Biol., 46, 269, 10.1016/0022-2836(69)90421-5
Lifson, 1968, A consistent force field for calculation on conformations, vibrational spectra and enthalpies of cycloalkanes and n-alkane molecules, J. Phys. Chem, 49, 5116, 10.1063/1.1670007
Malde, 2011, An automated force field topology builder (ATB) and repository: version 1.0, J. Chem. Theor. Comput., 7, 4026, 10.1021/ct200196m
Marrink, 2007, The MARTINI force field: Coarse grained model for biomolecular simulations, J. Phys. Chem. B, 111, 7812, 10.1021/jp071097f
Martyna, 1996, Explicit reversible integrators for extended systems dynamics, Mol. Phys., 87, 1117, 10.1080/00268979600100761
Murail, 2011, Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor, Biophys J., 100, 1642, 10.1016/j.bpj.2011.02.032
Noé, 2008, Transition networks for modeling the kinetics of conformational change in macromolecules, Curr. Opin. Struct. Biol., 18, 154, 10.1016/j.sbi.2008.01.008
Nosé, 1983, Constant pressure molecular dynamics for molecular systems, Mol. Phys., 50, 1055, 10.1080/00268978300102851
Nury, 2010, One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue, Proc. Natl Acad. Sci. USA, 107, 6275, 10.1073/pnas.1001832107
Onufriev, 2004, Exploring protein native states and large-scale conformational changes with a modified generalized born model, Proteins, 55, 383, 10.1002/prot.20033
Pande, 2010, Everything you wanted to know about Markov state models but were afraid to ask, Methods, 52, 99, 10.1016/j.ymeth.2010.06.002
Parrinello, 1981, Polymorphic transitions in single crystals: a new molecular dynamics method, J. Appl. Phys., 52, 7182, 10.1063/1.328693
Qui, 1997, The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii, J. Phys. Chem. A, 101, 3005, 10.1021/jp961992r
Schulz, 2009, Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supercomputer, J. Chem. Theor. Comput., 5, 2798, 10.1021/ct900292r
Shirts, 2005, Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration, J. Chem. Phys., 122, 144107, 10.1063/1.1873592
Swope, 1982, A computer-simulation method for the calculation of equilibrium-constants for the formation of physical clusters of molecules: application to small water clusters, J. Chem. Phys., 76, 637, 10.1063/1.442716
Valiev, 2010, NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations, Comput. Phys. Commun., 181, 1477, 10.1016/j.cpc.2010.04.018
van der Spoel, 2006, Protein folding kinetics and thermodynamics from atomistic simulations, Phys. Rev. Lett., 96, 238102, 10.1103/PhysRevLett.96.238102
van der Spoel, 2006, The origin of layer structure artifacts in simulations of liquid water, J. Chem. Theor. Comput., 2, 1, 10.1021/ct0502256
van der Spoel, 2012, GROMACS molecule and liquid database, Bioinformatics, 28, 752, 10.1093/bioinformatics/bts020
Vanommeslaeghe, 2010, CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields, J. Comput. Chem., 31, 671, 10.1002/jcc.21367
Wang, 2005, Antechamber, an accessory software package for molecular mechanical calculations, J. Comput. Chem., 25, 1157, 10.1002/jcc.20035
Wold, 2010, g_membed: efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation, J. Comp. Chem., 31, 2169, 10.1002/jcc.21507