Derivation of sensitive discrimination potential for virtual ligand screening

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[1]  F E Cohen,et al.  Modeling protein-ligand complexes. , 1996, Current opinion in structural biology.

[2]  Ruben Abagyan,et al.  ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..

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

[4]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .

[5]  J A McCammon,et al.  Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. , 1994, Journal of molecular biology.

[6]  S Vajda,et al.  Flexible docking and design. , 1995, Annual review of biophysics and biomolecular structure.

[7]  S. Sriharan,et al.  The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems , 1995, J. Comput. Chem..

[8]  Brian K. Shoichet,et al.  Molecular docking using shape descriptors , 1992 .

[9]  R Abagyan,et al.  Flexible protein–ligand docking by global energy optimization in internal coordinates , 1997, Proteins.

[10]  Thomas Lengauer,et al.  Computational methods for biomolecular docking. , 1996, Current opinion in structural biology.

[11]  T. Halgren Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[12]  Robert P. Sheridan,et al.  FLOG: A system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[13]  F. A. Seiler,et al.  Numerical Recipes in C: The Art of Scientific Computing , 1989 .

[14]  H. Berendsen,et al.  The electric potential of a macromolecule in a solvent: A fundamental approach , 1991 .

[15]  M J Sternberg,et al.  A continuum model for protein-protein interactions: application to the docking problem. , 1995, Journal of molecular biology.

[16]  J. Briggs,et al.  Structure-based drug design: computational advances. , 1997, Annual review of pharmacology and toxicology.

[17]  J. Janin,et al.  Protein-protein recognition. , 1995, Progress in biophysics and molecular biology.

[18]  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 .

[19]  I. Kuntz,et al.  Structure-based discovery of inhibitors of thymidylate synthase. , 1993, Science.