Thirty-five years of biomolecular simulation: development of methodology, force fields and software

Computer simulation of biomolecular systems has become a standard research instrument for the investigation of biomolecular processes at the atomic level of modelling and interpretation. A bird's eye view of the development of simulation methodology, of biomolecular interaction functions and simulation software is presented, together with the challenges in regard to these three aspects of biomolecular simulation.

[1]  H. Berendsen,et al.  ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS , 1977 .

[2]  Wilfred F. van Gunsteren,et al.  Interfacing the GROMOS (bio)molecular simulation software to quantum‐chemical program packages , 2012, J. Comput. Chem..

[3]  F. Stillinger,et al.  Molecular Dynamics Study of Liquid Water , 1971 .

[4]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[5]  Wilfred F. van Gunsteren,et al.  SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics , 1998 .

[6]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[7]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[8]  Margaret E. Johnson,et al.  Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.

[9]  Chris Oostenbrink,et al.  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..

[10]  J. Perram,et al.  Angular correlation functions in the mean spherical model , 1977 .

[11]  C. Schiffer,et al.  Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system. , 1995, Acta crystallographica. Section D, Biological crystallography.

[12]  W. V. van Gunsteren,et al.  Prediction of folding equilibria of differently substituted peptides using one-step perturbation. , 2010, Journal of the American Chemical Society.

[13]  R W Hockney,et al.  Computer Simulation Using Particles , 1966 .

[14]  Y. Sugita,et al.  Multidimensional replica-exchange method for free-energy calculations , 2000, cond-mat/0009120.

[15]  X. Daura,et al.  Parametrization of aliphatic CHn united atoms of GROMOS96 force field , 1998 .

[16]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[17]  Alan E. Mark,et al.  Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State , 1996 .

[18]  M. Levitt,et al.  Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .

[19]  Jane R. Allison,et al.  A method to explore protein side chain conformational variability using experimental data. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.

[20]  T. Schneider,et al.  Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions , 1978 .

[21]  Wilfred F. van Gunsteren,et al.  Lattice‐sum methods for calculating electrostatic interactions in molecular simulations , 1995 .

[22]  Andrew E. Torda,et al.  Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics , 1997 .

[23]  Aneesur Rahman,et al.  Correlations in the Motion of Atoms in Liquid Argon , 1964 .

[24]  Harold A. Scheraga,et al.  Intermolecular potentials from crystal data. III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines, and amides , 1974 .

[25]  Peter A. Kollman,et al.  AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .

[26]  Andrew E. Torda,et al.  The GROMOS biomolecular simulation program package , 1999 .

[27]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[28]  Arieh Warshel,et al.  Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs , 1993, J. Comput. Chem..

[29]  Charles L. Brooks,et al.  CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations , 2004, J. Comput. Chem..

[30]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[31]  Wilfred F van Gunsteren,et al.  Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. , 2006, The Journal of chemical physics.

[32]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[33]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[34]  Andrew E. Torda,et al.  Local elevation: A method for improving the searching properties of molecular dynamics simulation , 1994, J. Comput. Aided Mol. Des..

[35]  Bergström,et al.  Large-pT production of D-wave quarkonium states at hadron colliders. , 1992, Physical review. D, Particles and fields.

[36]  Markus Christen,et al.  The GROMOS software for biomolecular simulation: GROMOS05 , 2005, J. Comput. Chem..

[37]  S. Lifson,et al.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.

[38]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[39]  Richard A. Friesner,et al.  Integrated Modeling Program, Applied Chemical Theory (IMPACT) , 2005, J. Comput. Chem..

[40]  Alexander D. MacKerell,et al.  Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. , 2005, Journal of chemical theory and computation.

[41]  Walter Thiel,et al.  On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations , 2012, J. Comput. Chem..

[42]  Alan E. Mark,et al.  The GROMOS96 Manual and User Guide , 1996 .

[43]  H. Scheraga,et al.  On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method , 1989 .

[44]  W. V. Gunsteren,et al.  A modular molecular dynamics / quantum dynamics program for non-adiabatic proton transfers in solution , 1997 .

[45]  W. F. Gunsteren,et al.  Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble , 1995, Journal of biomolecular NMR.

[46]  H. Scheraga,et al.  Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides , 1994 .

[47]  Jane R. Allison,et al.  Biomolecular structure refinement using the GROMOS simulation software , 2011, Journal of biomolecular NMR.

[48]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[49]  M. Levitt,et al.  Molecular dynamics of native protein. I. Computer simulation of trajectories. , 1983, Journal of molecular biology.

[50]  M. Levitt,et al.  Refinement of protein conformations using a macromolecular energy minimization procedure. , 1969, Journal of molecular biology.

[51]  R. Zwanzig High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[52]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[53]  Julien Michel,et al.  Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. , 2008, The journal of physical chemistry. B.

[54]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[55]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[56]  Wilfred F. van Gunsteren,et al.  Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation , 2009, J. Comput. Chem..

[57]  Wilfred F. van Gunsteren,et al.  New functionalities in the GROMOS biomolecular simulation software , 2012, J. Comput. Chem..

[58]  Qiang Shi,et al.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. , 2006, The journal of physical chemistry. B.

[59]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[60]  Markus Christen,et al.  Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation , 2012, Comput. Phys. Commun..

[61]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[62]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[63]  Wilfred F. van Gunsteren,et al.  One-Step Perturbation Methods for Solvation Free Energies of Polar Solutes , 2001 .

[64]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[65]  Wilfred F. van Gunsteren,et al.  Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin–DNA duplex complexes in aqueous solution , 2012, J. Comput. Chem..

[66]  Wilfred F van Gunsteren,et al.  Free energies of ligand binding for structurally diverse compounds. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Wilfred F. van Gunsteren,et al.  A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software , 2010, J. Comput. Chem..

[68]  W. F. van Gunsteren,et al.  Effect of constraints on the dynamics of macromolecules , 1982 .

[69]  J. Kirkwood Quantum Statistics of Almost Classical Assemblies , 1933 .

[70]  W. F. Gunsteren,et al.  Crystallographic Refinement and Structure-Factor Time-Averaging by Molecular Dynamics in the Absence of a Physical Force Field , 1993 .

[71]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[72]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[73]  C. Schiffer,et al.  Accessibility and order of water sites in and around proteins: A crystallographic time‐averaging study , 1999, Proteins.

[74]  B. Brooks,et al.  Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .

[75]  Wilfred F van Gunsteren,et al.  Enveloping distribution sampling: a method to calculate free energy differences from a single simulation. , 2007, The Journal of chemical physics.

[76]  L. Verlet Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[77]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[78]  H. C. Andersen Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[79]  Enrico Clementi,et al.  Methods and techniques in computational chemistry : METECC-95 , 1995 .

[80]  R. Hockney The potential calculation and some applications , 1970 .

[81]  S. Nosé A molecular dynamics method for simulations in the canonical ensemble , 1984 .

[82]  Wilfred F van Gunsteren,et al.  Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. , 2011, The journal of physical chemistry. B.

[83]  Chris Oostenbrink,et al.  An improved nucleic acid parameter set for the GROMOS force field , 2005, J. Comput. Chem..

[84]  M. Parrinello,et al.  Crystal structure and pair potentials: A molecular-dynamics study , 1980 .

[85]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[86]  Andreas P. Eichenberger,et al.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7 , 2011, European Biophysics Journal.

[87]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[88]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[89]  W. V. van Gunsteren,et al.  Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. , 1990, Journal of molecular biology.

[90]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[91]  Wilfred F van Gunsteren,et al.  GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. , 2011, Journal of chemical theory and computation.

[92]  W. F. Gunsteren,et al.  Time-dependent distance restraints in molecular dynamics simulations , 1989 .

[93]  Norman L. Allinger,et al.  Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms , 1977 .

[94]  W. F. van Gunsteren,et al.  Computer Simulation of Proton Transfers of Small Acids in Water , 2000 .

[95]  C. Oostenbrink,et al.  On using oscillating time-dependent restraints in MD simulation , 2007, Journal of biomolecular NMR.

[96]  Wilfred F van Gunsteren,et al.  On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm. , 2007, The Journal of chemical physics.

[97]  Wilfred F. van Gunsteren,et al.  An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase , 2001, J. Comput. Chem..

[98]  Siewert J Marrink,et al.  Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. , 2011, Physical chemistry chemical physics : PCCP.

[99]  W F van Gunsteren,et al.  A protein structure from nuclear magnetic resonance data. lac repressor headpiece. , 1985, Journal of molecular biology.

[100]  Jonathan W. Essex,et al.  The development of replica-exchange-based free-energy methods , 2003 .

[101]  R. Larson,et al.  The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.

[102]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[103]  B. Widom,et al.  Some Topics in the Theory of Fluids , 1963 .