A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules

[1]  Gordon M. Crippen,et al.  Conformational analysis by scaled energy embedding , 1984 .

[2]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[3]  T. Hayden,et al.  Prediction of DNA structure from sequence: A build‐up technique , 1989, Biopolymers.

[4]  J. Stewart Semiempirical Molecular Orbital Methods , 2007 .

[5]  Harold A. Scheraga,et al.  Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability‐directed search procedure , 1989 .

[6]  A. Gronenborn,et al.  Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. , 1988, Protein engineering.

[7]  Andrew R. Leach,et al.  Automated conformational analysis and structure generation: algorithms for molecular perception , 1990, J. Chem. Inf. Comput. Sci..

[8]  Garland R. Marshall,et al.  Constrained search of conformational hyperspace , 1989, J. Comput. Aided Mol. Des..

[9]  W. C. Still,et al.  A rapid approximation to the solvent accessible surface areas of atoms , 1988 .

[10]  Martha W. Evens,et al.  Conformational analysis using a truth maintenance system , 1988 .

[11]  M. Karplus,et al.  Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[12]  D. Ferguson,et al.  Molecular mechanics conformational analysis of cyclononane using the RIPS method and comparison with quantum‐mechanical calculations , 1989 .

[13]  D. Barton,et al.  The conformation of the steroid nucleus , 1950, Experientia.

[14]  A potential function for conformational analysis of proteins. , 2009, International journal of peptide and protein research.

[15]  Keith Prout,et al.  Automated conformational analysis: Algorithms for the efficient construction of low-energy conformations , 1990, J. Comput. Aided Mol. Des..

[16]  M J Sternberg,et al.  A relational database of protein structures designed for flexible enquiries about conformation. , 1989, Protein engineering.

[17]  H. Scheraga,et al.  Pattern recognition in the prediction of protein structure. I. Tripeptide conformational probabilities calculated from the amino acid sequence , 1989 .

[18]  I. Kuntz,et al.  [9] Distance geometry , 1989 .

[19]  D. Ferguson,et al.  Molecular mechanics calculations of several lanthanide complexes: An application of the random incremental pulse search , 1990 .

[20]  F. Allen,et al.  The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information , 1979 .

[21]  Gordon M. Crippen,et al.  Residue-residue potential function for conformational analysis of proteins , 1981 .

[22]  W. C. Still,et al.  The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space , 1988 .

[23]  Bernard R. Brooks,et al.  Applications of Molecular Dynamics for Structural Analysis of Proteins and Peptides , 1987 .

[24]  A. Brunger Crystallographic refinement by simulated annealing , 1988 .

[25]  A. Pardi,et al.  Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data. , 1989, Biochemistry.

[26]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[27]  H. Scheraga,et al.  Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. I. Backbone structure of enkephalin , 1985, Biopolymers.

[28]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[29]  Martin Saunders,et al.  Conformations of cycloheptadecane. A comparison of methods for conformational searching , 1990 .

[30]  Klaus Gubernator,et al.  Generic shapes for the conformation analysis of macrocyclic structures , 1988 .

[31]  G. M. Crippen,et al.  Why energy embedding works , 1987 .

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

[33]  R. J. Williams,et al.  Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry. , 1990, Journal of molecular biology.

[34]  T. L. Blundell,et al.  Knowledge-based prediction of protein structures and the design of novel molecules , 1987, Nature.

[35]  D. B. Boyd Space-filling molecular models of four-membered rings. Three-dimensional aspects in the design of penicillin and cephalosporin antibiotics. , 1976, Journal of chemical education.

[36]  I. Kuntz,et al.  Tertiary Structure Prediction , 1989 .

[37]  Peter Murray-Rust,et al.  Computer retrieval and analysis of molecular geometry. III. Geometry of the β-1'-aminofuranoside fragment , 1978 .

[38]  G. Chang,et al.  An internal-coordinate Monte Carlo method for searching conformational space , 1989 .

[39]  The use of stochastic search in looking for homeomorphic isomerism: synthesis and properties of bicyclo[6.5.1]tetradecane , 1990 .

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

[41]  N Go,et al.  Efficient monte carlo method for simulation of fluctuating conformations of native proteins , 1985, Biopolymers.

[42]  H. Scheraga,et al.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Harold A. Scheraga,et al.  Pattern recognition in the prediction of protein structure. III. An importance‐sampling minimization procedure , 1989 .

[44]  Gordon M. Crippen,et al.  Stable calculation of coordinates from distance information , 1978 .

[45]  R J Read,et al.  Critical evaluation of comparative model building of Streptomyces griseus trypsin. , 1984, Biochemistry.

[46]  Robin Taylor The Cambridge Structural Database in molecular graphics: techniques for the rapid identification of conformational minima , 1986 .

[47]  Timothy F. Havel,et al.  A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular1H−1H proximities in solution , 1984 .

[48]  Martin Saunders,et al.  Stochastic search for the conformations of bicyclic hydrocarbons , 1989 .

[49]  H. Scheraga,et al.  Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .

[50]  Peter Murray-Rust,et al.  Computer analysis of molecular geometry: Part VI: Classification of differences in conformation , 1985 .

[51]  J. Thornton,et al.  Protein motifs and data-base searching. , 1989, Trends in biochemical sciences.

[52]  G. Crippen,et al.  Determination of an empirical energy function for protein conformational analysis by energy embedding , 1987 .

[53]  P. D. Clercq,et al.  Systematic conformational analysis. A microcomputer method for the semiquantitative evaluation of polycyclic systems containing five-, six- and seven-membered rings. 1. Program characteristics. , 1984 .

[54]  J. Moult,et al.  An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.

[55]  Andrew R. Leach,et al.  WIZARD: AI in conformational analysis , 1987, J. Comput. Aided Mol. Des..

[56]  H A Scheraga,et al.  An approach to the multiple-minima problem by relaxing dimensionality. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[57]  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 .

[58]  V N Viswanadhan,et al.  Sidechain and backbone potential function for conformational analysis of proteins. , 1985, International journal of peptide and protein research.

[59]  R. Taylor CAMAL– a new component of the Cambridge Structural Database software system , 1986 .

[60]  Harold A. Scheraga,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops , 1990 .

[61]  Martin Saunders,et al.  A New Method for Molecular Mechanics , 1986 .

[62]  Kurt Wüthrich,et al.  The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization , 1987 .

[63]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures , 1987, Biopolymers.

[64]  N. Cohen,et al.  Script: interactive molecular geometrical treatments on the basis of computer-drawn chemical formula , 1981 .

[65]  D F Veber,et al.  Computer-aided, systematic search of peptide conformations constrained by NMR data. , 1986, Biochemical and biophysical research communications.

[66]  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.

[67]  M. Summers,et al.  High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach. , 1990, Biochemistry.

[68]  Systematic conformational analysis. A microcomputer method for the semiquantitative evaluation of polycyclic systems containing five-, six- and seven-membered rings. 2. Scope and limitations. , 1984 .

[69]  M Karplus,et al.  Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Timothy F. Havel,et al.  The theory and practice of distance geometry , 1983, Bulletin of Mathematical Biology.

[71]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[72]  Ioan Motoc,et al.  Three-Dimensional Quantitative Structure-Activity Relationships I. General Approach to the Pharmacophore Model Validation† , 1986 .

[73]  Irwin D. Kuntz,et al.  A new technique to calculate low-energy conformations of cyclic molecules utilizing the ellipsoid algorithm and molecular dynamics: application to 18-crown-6 , 1988 .

[74]  N Go,et al.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.

[75]  C. Levinthal,et al.  Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations , 1986, Proteins.

[76]  O. Hassel Stereochemistry of cyclohexane. , 1950, Research; a journal of science and its applications.

[77]  N. Go,et al.  Dynamics of a small globular protein in terms of low-frequency vibrational modes. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[78]  N. Go,et al.  Ring Closure and Local Conformational Deformations of Chain Molecules , 1970 .

[79]  Georges Wipff,et al.  High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic “222” cryptand , 1990 .

[80]  Peter Murray-Rust,et al.  Computer retrieval and analysis of molecular geometry. II. Variance and its interpretation , 1978 .

[81]  H. Scheraga,et al.  Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. , 1988, Journal of biomolecular structure & dynamics.

[82]  H. Scheraga,et al.  Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids , 1983 .

[83]  T. A. Jones,et al.  A graphics model building and refinement system for macromolecules , 1978 .

[84]  M. Levitt Protein folding by restrained energy minimization and molecular dynamics. , 1983, Journal of molecular biology.

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

[86]  N Go,et al.  Structural basis of hierarchical multiple substates of a protein. I: Introduction , 1989, Proteins.

[87]  Stephen R. Wilson,et al.  Conformational Analysis of Flexible Molecules: Location of the Global Minimum Energy Conformation by the Simulated Annealing Method , 1988 .

[88]  M. Karplus,et al.  Conformational sampling using high‐temperature molecular dynamics , 1990, Biopolymers.

[89]  C. R. Ganellin,et al.  Calculation of conformational free energy of histamine , 1974 .

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

[91]  Andrew R. Leach,et al.  An investigation into the construction of molecular models by the template joining method , 1988, J. Comput. Aided Mol. Des..

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

[93]  S. Wilson,et al.  Applications of simulated annealing to peptides , 1990, Biopolymers.

[94]  V. Cerný Thermodynamical approach to the traveling salesman problem: An efficient simulation algorithm , 1985 .

[95]  Karl Menger,et al.  New Foundation of Euclidean Geometry , 1931 .

[96]  Gordon M. Crippen,et al.  Note rapid calculation of coordinates from distance matrices , 1978 .

[97]  H A Scheraga,et al.  Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. , 1988, Journal of biomolecular structure & dynamics.

[98]  Robert Hooke,et al.  `` Direct Search'' Solution of Numerical and Statistical Problems , 1961, JACM.

[99]  Peter Murray-Rust,et al.  Computer retrieval and analysis of molecular geometry. I. General principles and methods , 1978 .

[100]  H. Scheraga,et al.  Use of buildup and energy‐minimization procedures to compute low‐energy structures of the backbone of enkephalin , 1985, Biopolymers.

[101]  Harold A. Scheraga,et al.  The multiple-minima problem in the conformational analysis of polypeptides. III. An Electrostatically Driven Monte Carlo Method: Tests on enkephalin , 1989, Journal of protein chemistry.

[102]  T. Sejnowski,et al.  Predicting the secondary structure of globular proteins using neural network models. , 1988, Journal of molecular biology.

[103]  H A Scheraga,et al.  Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. III. Probable and average conformations of enkephalin , 1987, Biopolymers.

[104]  Gordon M. Crippen,et al.  Global energy minimization by rotational energy embedding , 1990, J. Chem. Inf. Comput. Sci..

[105]  H A Scheraga,et al.  On the multiple‐minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed α‐helix , 1987 .

[106]  Daniel P. Dolata,et al.  WIZARD: applications of expert system techniques to conformational analysis. 1. The basic algorithms exemplified on simple hydrocarbons , 1987, J. Chem. Inf. Comput. Sci..

[107]  R H Reid,et al.  Computer simulations of a tumor surface octapeptide epitope , 1989, Biopolymers.

[108]  Robert E. Bruccoleri,et al.  Chain closure with bond angle variations , 1985 .

[109]  Timothy F. Havel,et al.  The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations , 1990, Biopolymers.

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

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

[112]  G M Crippen,et al.  A 1.8 Å resolution potential function for protein folding , 1990, Biopolymers.

[113]  R. Kaptein,et al.  The solution structure of the intramolecular photoproduct of d(TpA) derived with the use of NMR and a combination of distance geometry and molecular dynamics. , 1990, Nucleic acids research.

[114]  C. Cori,et al.  Correction of a genetically caused enzyme defect by somatic cell hybridization. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[115]  Jiří Novotný,et al.  Structure of antibody hypervariable loops reproduced by a conformational search algorithm , 1988, Nature.

[116]  H. Scheraga,et al.  On the multiple‐minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method—tests on poly(L‐alanine) , 1988, Biopolymers.

[117]  Harold A. Scheraga,et al.  Free energies of hydration of solute molecules. 3. Application of the hydration shell model to charged organic molecules , 1987 .

[118]  C. DeLisi,et al.  Determining minimum energy conformations of polypeptides by dynamic programming , 1990, Biopolymers.

[119]  M. Saunders Stochastic exploration of molecular mechanics energy surfaces. Hunting for the global minimum , 1987 .

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

[121]  E. Olejniczak,et al.  Structure refinement of a cyclic peptide from two-dimensional NMR data and molecular modeling. , 1987, Biochemistry.

[122]  D. Ferguson,et al.  Structures of lanthanide shift reagent complexes by molecular mechanics computations , 1985 .

[123]  Robert Langridge,et al.  A distance geometry study of ring systems , 1983 .

[124]  Gordon M. Crippen,et al.  Conformational analysis by energy embedding , 1982 .

[125]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[126]  D. Ferguson,et al.  A new approach to probing conformational space with molecular mechanics: Random incremental pulse search , 1989 .

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

[128]  N. Go Shape of the conformational energy surface near the global minimum and low‐frequency vibrations in the native conformation of globular proteins , 1978 .

[129]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[130]  W. Clark Still,et al.  Chemical consequences of conformation in macrocyclic compounds , 1981 .

[131]  H A Scheraga,et al.  An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin. , 1987, Journal of molecular biology.

[132]  Harold A. Scheraga,et al.  Free energies of hydration of solute molecules. 1. Improvement of the hydration shell model by exact computations of overlapping volumes , 1987 .

[133]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[134]  H. Scheraga,et al.  Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry , 1990 .

[135]  M. Karplus,et al.  Advances in chemical physics, volume 71: Proteins: A theoretical perspective of dynamics, structure, and thermodynamics , 2006 .

[136]  J M Blaney,et al.  Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A. , 2009, International journal of peptide and protein research.

[137]  Keith Prout,et al.  The application of Artificial Intelligence to the conformational analysis of strained molecules , 1990 .

[138]  Andrew R. Leach,et al.  Automated conformational analysis: Directed conformational search using the A* algorithm , 1990 .

[139]  W. L. Koltun,et al.  Precision space‐filling atomic models , 1965, Biopolymers.

[140]  H. Scheraga Theoretical and experimental studies of conformations of polypeptides. , 1971, Chemical reviews.