Conformational Analysis and Searching

[1]  H. Berendsen,et al.  A consistent empirical potential for water–protein interactions , 1984 .

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

[3]  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.

[4]  T. Lybrand Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods , 2007 .

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

[6]  P. Sprague Automated chemical hypothesis generation and database searching with Catalyst , 1995 .

[7]  J. Gasteiger,et al.  FROM ATOMS AND BONDS TO THREE-DIMENSIONAL ATOMIC COORDINATES : AUTOMATIC MODEL BUILDERS , 1993 .

[8]  Jan Hoflack,et al.  The sca program : an easy way for the conformational evaluation of polycyclic molecules , 1988 .

[9]  Gerhard Klebe,et al.  Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors , 1994, J. Comput. Aided Mol. Des..

[10]  X. Daura,et al.  The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation. , 2001, Journal of the American Chemical Society.

[11]  Johann Gasteiger,et al.  Ein automatisierter Molekülbaukasten , 1987 .

[12]  H. Scheraga,et al.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Andrew Smellie,et al.  Analysis of Conformational Coverage, 1. Validation and Estimation of Coverage , 1995, J. Chem. Inf. Comput. Sci..

[14]  Jonas Boström,et al.  Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools , 2001, J. Comput. Aided Mol. Des..

[15]  Dennis H. Smith,et al.  Deriving three-dimensional representations of molecular structure from connection tables augmented with configuration designations using distance geometry , 1982, J. Chem. Inf. Comput. Sci..

[16]  Johann Gasteiger,et al.  The Search for the Spatial and Electronic Requirements of a Drug , 2000 .

[17]  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 .

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

[19]  F. A. Neugebauer,et al.  Electrochemical oxidation and structural changes of 5,6-dihydrobenzo[c]cinnolines , 1996 .

[20]  Owen Johnson,et al.  The development of versions 3 and 4 of the Cambridge Structural Database System , 1991, J. Chem. Inf. Comput. Sci..

[21]  J. S. Dixon,et al.  Distance Geometry in Molecular Modeling , 2007 .

[22]  P. D. Clercq Correction. Systematic Conformational Analysis. General Method for Rapid Conformational Evaluation. Its Application to the Hydroazulene System , 1981 .

[23]  J. Gasteiger,et al.  Automatic generation of 3D-atomic coordinates for organic molecules , 1990 .

[24]  Bradley D. Christie,et al.  Building 3D structural databases: Experiences with MDDR-3D and FCD-3D , 1990 .

[25]  Johann Gasteiger,et al.  Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method , 1998, J. Chem. Inf. Comput. Sci..

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

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

[28]  Jens Sadowski,et al.  A hybrid approach for addressing ring flexibility in 3D database searching , 1997, J. Comput. Aided Mol. Des..

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

[30]  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.

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

[32]  Gerhard Klebe,et al.  Structure Correlation and Ligand/Receptor Interactions , 1994 .

[33]  Eiji Osawa,et al.  Corner flapping: a simple and fast algorithm for exhaustive generation of ring conformations , 1989 .

[34]  Harold A. Scheraga,et al.  Predicting Three‐Dimensional Structures of Oligopeptides , 2007 .

[35]  Andrew Smellie,et al.  Poling: Promoting conformational variation , 1995, J. Comput. Chem..

[36]  Jonathan M. Goodman,et al.  Genetic Algorithms in Conformational Analysis , 1998, J. Chem. Inf. Comput. Sci..

[37]  D. Rognan,et al.  Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. , 2000, Journal of medicinal chemistry.

[38]  Gerhard Klebe,et al.  Methodological developments and strategies for a fast flexible superposition of drug-size molecules , 1999, J. Comput. Aided Mol. Des..

[39]  Tad Hurst,et al.  Flexible 3D searching: The directed tweak technique , 1994, J. Chem. Inf. Comput. Sci..

[40]  Gerhard Klebe,et al.  A fast and efficient method to generate biologically relevant conformations , 1994, J. Comput. Aided Mol. Des..

[41]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

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

[43]  P. D. Clercq,et al.  Systematic conformational analysis. torsion constraint evaluation in cyclic systems , 1981 .

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

[45]  J. Gasteiger,et al.  The generation of 3D models of host-guest complexes , 1992 .

[46]  Gerhard Klebe,et al.  Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures , 1994, J. Chem. Inf. Comput. Sci..

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

[48]  Patrick Bultinck,et al.  Generate: A program for 3‐D structure generation and conformational analysis of peptides and peptidomimetics , 2002, J. Comput. Chem..

[49]  Andrew R. Leach An Algorithm To Directly Identify a Molecule's "Most Different" Conformations , 1994, J. Chem. Inf. Comput. Sci..

[50]  Colin McMartin,et al.  QXP: Powerful, rapid computer algorithms for structure-based drug design , 1997, J. Comput. Aided Mol. Des..

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

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