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