Conformational sampling via a self-regulating effective energy surface.
暂无分享,去创建一个
Wei Yang | Aaron R Dinner | Martin Karplus | Ryan Bitetti-Putzer | M. Karplus | Wei Yang | A. Dinner | Ryan Bitetti-Putzer
[1] 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 .
[2] Amedeo Caflisch,et al. Computational combinatorial chemistry for de novo ligand design: Review and assessment , 1995 .
[3] S. Nosé. A molecular dynamics method for simulations in the canonical ensemble , 1984 .
[4] A. Voter,et al. Extending the Time Scale in Atomistic Simulation of Materials Annual Re-views in Materials Research , 2002 .
[5] Christian Bartels,et al. Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations , 1997 .
[6] U. Hansmann. Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.
[7] P A Kollman,et al. Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations. , 1999, Journal of medicinal chemistry.
[8] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[9] M. Karplus,et al. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics , 1988 .
[10] Charles L. Brooks,et al. Rapid Screening of Binding Affinities: Application of the λ-Dynamics Method to a Trypsin-Inhibitor System , 1998 .
[11] E. Bauer. Method of Calculating Cross Sections for Molecular Collisions , 1955 .
[12] Martin Karplus,et al. Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy , 1998 .
[13] M. Karplus,et al. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics , 1997 .
[14] Charles L. Brooks,et al. λ‐dynamics: A new approach to free energy calculations , 1996 .
[15] M. Karplus,et al. Self-guided enhanced sampling methods for thermodynamic averages , 2003 .
[16] M. Karplus,et al. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin , 1990 .
[17] G Stolovitzky,et al. Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[18] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[19] Bruce J. Berne,et al. Method for accelerating chain folding and mixing , 1993 .
[20] Aaron R. Dinner,et al. Monte Carlo simulations of biomolecules: The MC module in CHARMM , 2006, J. Comput. Chem..
[21] Straub,et al. Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[22] I. Andricioaei,et al. On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters , 1997 .
[23] M. Karplus,et al. Simulation of activation free energies in molecular systems , 1996 .
[24] Charles L. Brooks,et al. Efficient and Flexible Algorithm for Free Energy Calculations Using the λ-Dynamics Approach , 1998 .
[25] J.-P. Wery,et al. Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2 , 1995, Nature Structural Biology.
[26] Christian Bartels,et al. Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling , 1999 .
[27] J. J. Rosa,et al. Structures of free and inhibited human secretory phospholipase A2 from inflammatory exudate. , 1993, Science.
[28] Lee,et al. New Monte Carlo algorithm: Entropic sampling. , 1993, Physical review letters.
[29] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[30] Charles L. Brooks,et al. Application of Multiple Topology λ-Dynamics to a Host−Guest System: β-Cyclodextrin with Substituted Benzenes , 2001 .
[31] Bruce Tidor,et al. Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte Carlo approach , 1993 .
[32] Berg,et al. Multicanonical ensemble: A new approach to simulate first-order phase transitions. , 1992, Physical review letters.
[33] D. L. Freeman,et al. Reducing Quasi-Ergodic Behavior in Monte Carlo Simulations by J-Walking: Applications to Atomic Clusters , 1990 .
[34] Charles L. Brooks,et al. Free energy screening of small ligands binding to an artificial protein cavity , 2000 .
[35] B. Brooks,et al. Self-guided Langevin dynamics simulation method , 2003 .
[36] M. Karplus,et al. Functionality maps of binding sites: A multiple copy simultaneous search method , 1991, Proteins.
[37] R. Elber,et al. Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations , 1991 .
[38] Peter A. Kollman,et al. Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball” , 1998 .
[39] M. Karplus,et al. Advances in chemical physics, volume 71: Proteins: A theoretical perspective of dynamics, structure, and thermodynamics , 2006 .
[40] Sidney Yip,et al. Optimized free-energy evaluation using a single reversible-scaling simulation , 1999 .
[41] Alan E. Mark,et al. Calculation of Relative Free-Energy Via Indirect Pathways , 1991 .
[42] Bruce J. Berne,et al. Multicanonical jump walking: A method for efficiently sampling rough energy landscapes , 1999 .
[43] Xiongwu Wu,et al. Enhancing systematic motion in molecular dynamics simulation , 1999 .