Chapter 21 - Ways and Means to Enhance the Configurational Sampling of Small Peptides in Aqueous Solution in Molecular Dynamics Simulations

[1]  H. Weinstein,et al.  Conformational Memories and the Exploration of Biologically Relevant Peptide Conformations: An Illustration for the Gonadotropin-Releasing Hormone , 1996 .

[2]  W. V. van Gunsteren,et al.  An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. , 1996, Journal of molecular biology.

[3]  Molecular dynamics simulation of despentapeptide insulin in a crystalline environment. , 1988 .

[4]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[5]  H J Berendsen,et al.  An efficient method for sampling the essential subspace of proteins. , 1996, Journal of biomolecular structure & dynamics.

[6]  K. Wüthrich,et al.  Nmr studies of the rates of proline cis–trans isomerization in oligopeptides , 1981 .

[7]  G Vriend,et al.  A novel search method for protein sequence--structure relations using property profiles. , 1994, Protein engineering.

[8]  Y. Okamoto,et al.  Numerical comparisons of three recently proposed algorithms in the protein folding problem , 1997 .

[9]  D. Yee,et al.  Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.

[10]  E I Shakhnovich,et al.  Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. , 1995, Journal of molecular biology.

[11]  R. Wade,et al.  Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis. , 1997, Folding & design.

[12]  J. Andrew McCammon,et al.  Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide , 1996 .

[13]  Klaus R. Liedl,et al.  Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics , 1996 .

[14]  Rebecca C. Wade,et al.  Use of Multiple Molecular Dynamics Trajectories To Study Biomolecules in Solution: The YTGP Peptide , 1998 .

[15]  Franca Fraternali,et al.  Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques , 1994 .

[16]  R Abagyan,et al.  Homology modeling by the ICM method , 1995, Proteins.

[17]  Shankar Kumar,et al.  Multidimensional free‐energy calculations using the weighted histogram analysis method , 1995, J. Comput. Chem..

[18]  R. Abagyan,et al.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.

[19]  C. Tsallis,et al.  Statistical-mechanical foundation of the ubiquity of Lévy distributions in Nature. , 1995, Physical review letters.

[20]  T. Creighton,et al.  The physical properties of local interactions of tyrosine residues in peptides and unfolded proteins. , 1995, Journal of molecular biology.

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

[22]  L. Verlet Computer "Experiments" on Classical Fluids. II. Equilibrium Correlation Functions , 1968 .

[23]  Temple F. Smith,et al.  Global optimum protein threading with gapped alignment and empirical pair score functions. , 1996, Journal of molecular biology.

[24]  T. Straatsma,et al.  ARGOS, a vectorized general molecular dynamics program , 1990 .

[25]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[26]  H. Berendsen,et al.  An extended sampling of the configurational space of HPr from E. coli , 1996, Proteins.

[27]  W. V. van Gunsteren,et al.  Conformational differences between alpha-cyclodextrin in aqueous solution and in crystalline form. A molecular dynamics study. , 1988, Journal of molecular biology.

[28]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[29]  New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997 .

[30]  Christian Bartels,et al.  Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations , 1997 .

[31]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

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

[33]  M K Gilson,et al.  Theory of electrostatic interactions in macromolecules. , 1995, Current opinion in structural biology.

[34]  C L Brooks,et al.  Calculations on folding of segment B1 of streptococcal protein G. , 1998, Journal of molecular biology.

[35]  B. Berne,et al.  A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems , 1995 .

[36]  Charles L. Brooks,et al.  Molecular picture of folding of a small α/β protein , 1998 .

[37]  W. F. Gunsteren,et al.  Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results , 1996 .

[38]  J A McCammon,et al.  Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. , 1993, Biophysical journal.

[39]  M Karplus,et al.  Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs , 1997, Proteins.

[40]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[41]  B. Berne,et al.  Novel methods of sampling phase space in the simulation of biological systems. , 1997, Current opinion in structural biology.

[42]  K. Wilson The renormalization group: Critical phenomena and the Kondo problem , 1975 .

[43]  R Elber,et al.  Computer determination of peptide conformations in water: different roads to structure. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

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

[45]  M. Karplus,et al.  PDB-based protein loop prediction: parameters for selection and methods for optimization. , 1997, Journal of molecular biology.

[46]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[47]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[48]  Arieh Warshel,et al.  CONTINUUM AND DIPOLE-LATTICE MODELS OF SOLVATION , 1997 .

[49]  Conformational dynamics of proteins: Beyond the nanosecond timescale. , 1994 .

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

[51]  P. Adams,et al.  New applications of simulated annealing in X-ray crystallography and solution NMR. , 1997, Structure.

[52]  A. Liwo,et al.  A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data , 1997 .

[53]  K. Schulten,et al.  Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics , 1997 .

[54]  T. P. Straatsma,et al.  Treatment of rotational isomeric states. III. The use of biasing potentials , 1994 .

[55]  James Andrew McCammon,et al.  Molecular dynamics simulation with a continuum electrostatic model of the solvent , 1995, J. Comput. Chem..

[56]  P. Weiner,et al.  Computer Simulation of Biomolecular Systems , 1997 .

[57]  Shankar Kumar,et al.  Method for free‐energy calculations using iterative techniques , 1996 .

[58]  Y. Okamoto Helix‐forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing , 1994, Proteins.

[59]  Harold A. Scheraga,et al.  Some approaches to the multiple-minima problem in protein folding , 1995, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding.

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

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

[62]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[63]  Michael K. Gilson,et al.  ''Mining minima'': Direct computation of conformational free energy , 1997 .

[64]  H. Scheraga,et al.  Revised algorithms for the build‐up procedure for predicting protein conformations by energy minimization , 1987 .

[65]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[66]  H. Orland,et al.  Biasing a Monte Carlo chain growth method with Ramachandran's plot: Application to twenty‐L‐alanine , 1993, Biopolymers.

[67]  Thirumalai,et al.  Ergodic behavior in supercooled liquids and in glasses. , 1989, Physical review. A, General physics.

[68]  D S Goodsell,et al.  Automated docking of flexible ligands: Applications of autodock , 1996, Journal of molecular recognition : JMR.

[69]  H J Berendsen,et al.  Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. , 1996, Journal of biomolecular structure & dynamics.

[70]  Benoît Roux,et al.  Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations , 1995 .

[71]  A. Liwo,et al.  A united‐residue force field for off‐lattice protein‐structure simulations. II. Parameterization of short‐range interactions and determination of weights of energy terms by Z‐score optimization , 1997 .

[72]  R Abagyan,et al.  A new method for modeling large‐scale rearrangements of protein domains , 1997, Proteins.

[73]  David C. Jones,et al.  Potential energy functions for threading. , 1996, Current opinion in structural biology.

[74]  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 .

[75]  Alan M. Ferrenberg,et al.  Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.

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

[77]  X. Daura,et al.  Studying the Stability of a Helical β‐Heptapeptide by Molecular Dynamics Simulations , 1997 .

[78]  R Elber,et al.  Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. , 1997, Journal of molecular biology.

[79]  A. Kidera,et al.  Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides , 1997 .

[80]  Grubmüller,et al.  Predicting slow structural transitions in macromolecular systems: Conformational flooding. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[81]  R Elber,et al.  Novel methods for molecular dynamics simulations. , 1996, Current opinion in structural biology.

[82]  R. Wade,et al.  The cisproline(i − 1)-aromatic(i) interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches , 2000, Journal of biomolecular NMR.

[83]  Daan Frenkel,et al.  Configurational bias Monte Carlo: a new sampling scheme for flexible chains , 1992 .

[84]  O. Steinhauser,et al.  Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. , 1992, Biochemistry.

[85]  B. Lee,et al.  Protein folding by a biased Monte Carlo procedure in the dihedral angle space , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[86]  Michel Peyrard,et al.  Nonlinear Excitations in Biomolecules , 1995 .

[87]  John W. Brady,et al.  Use of Umbrella Sampling in the Calculation of the Potential of Mean Force for Maltose in Vacuum From Molecular Dynamics Simulations , 1995 .

[88]  J Moult,et al.  Genetic algorithms for protein structure prediction. , 1996, Current opinion in structural biology.

[89]  C. Brooks,et al.  Exploring the folding free energy surface of a three-helix bundle protein. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[90]  M. Karplus,et al.  Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin , 1998, Protein science : a publication of the Protein Society.

[91]  D. Beglov,et al.  Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations , 1994 .

[92]  A. H. Juffer,et al.  DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS , 1993 .

[93]  T. Creighton,et al.  Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding. , 1993, Journal of molecular biology.