Computational methods for biomolecular docking

Lin, 1994, Molecular surface representation by sparse critical points, Proteins, 18, 94, 10.1002/prot.340180111

Norel, 1995, Molecular surface complementarity at protein—protein interfaces: the critical role played by surface normals at well placed sparse points in docking, J Mol Biol, 252, 263, 10.1006/jmbi.1995.0493

Vakser, 1994, Hydrophobic docking: a proposed enhancement to molecular recognition techniques, Proteins, 20, 320, 10.1002/prot.340200405

Ackermann, 1995, Protein docking combining symbolic descriptions of molecular surfaces and grid-based scoring functions, 3

Jiang, 1991, Soft docking: matching of molecular surface cubes, J Mol Biol, 219, 79, 10.1016/0022-2836(91)90859-5

Walls, 1992, New algorithm to model protein—protein recognition based on surface complementarity, J Mol Biol, 228, 277, 10.1016/0022-2836(92)90506-F

Helmer-Citterich, 1994, PUZZLE: a new method for automated protein docking based on surface shape complementarity, J Mol Biol, 235, 1021, 10.1006/jmbi.1994.1054

Duncan, 1994, Predicting protein—protein interactions using parametric surfaces

Shoichet, 1992, Molecular docking using shape descriptors, J Comput Chem, 13, 380, 10.1002/jcc.540130311

Fischer, 1995, A geometry-based suite of molecular docking processes, J Mol Biol, 248, 459, 10.1016/S0022-2836(95)80063-8

Lenhof, 1995, An algorithm for the protein docking problem, 125

Katchalski-Katzir, 1992, Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques, Proc Natl Acad Sci USA, 89, 2195, 10.1073/pnas.89.6.2195

Vakser, 1995, Protein docking for low-resolution structures, Protein Eng, 8, 371, 10.1093/protein/8.4.371

Totrov, 1994, Detailed ab initio prediction of lysozyme—antibody complex with 1.6 Å accuracy, Nat Struct Biol, 1, 259, 10.1038/nsb0494-259

Abagyan, 1994, Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins, J Mol Biol, 235, 983, 10.1006/jmbi.1994.1052

Halgren, 1995, Potential energy functions, Curr Opin Struct Biol, 5, 205, 10.1016/0959-440X(95)80077-8

Miller, 1994, FLOG: a system to select ‘quasi-flexible’ ligands complementary to a receptor to known three-dimensional structure, J Comput Aided Mol Des, 8, 153, 10.1007/BF00119865

Kearsley, 1994, Flexibases: a way to enhance the use of molecular docking methods, J Comput Aided Mol Des, 8, 565, 10.1007/BF00123666

Klebe, 1994, A fast and efficient method to generate biologically relevant conformations, J Comput Aided Mol Des, 8, 583, 10.1007/BF00123667

Böhm, 1994, The development of a simple empirical scoring function to estimate the binding constant for a protein—ligand complex of known three-dimensional structure, J Comput Aided Mol Des, 8, 243, 10.1007/BF00126743

Leach, 1992, Conformational analysis of flexible ligands in macromolecular receptor sites, J Comput Chem, 13, 730, 10.1002/jcc.540130608

Mizutani, 1994, Rational automatic search method for stable docking models of protein and ligand, J Mol Biol, 243, 310, 10.1006/jmbi.1994.1656

Rarey, 1995, Time-efficient docking of flexible ligands into active sites of proteins, 300

Sandak, 1995, An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching, Comput Appl Biosci, 11, 87

Clark, 1995, Flexible ligand docking without parameter adjustment across four ligand—receptor complexes, J Comput Chem, 16, 1210, 10.1002/jcc.540161004

Oshiro, 1995, Flexible ligand docking using a genetic algorithm, J Comput Aided Mol Des, 9, 113, 10.1007/BF00124402

Jones, 1995, Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation, J Mol Biol, 245, 43, 10.1016/S0022-2836(95)80037-9

Gelhaar, 1995, Docking conformationally flexible small molecules into a protein binding site through evolutionary programming, 615

Koshland, 1993, The joys and vicissitudes of protein science, Protein Sci, 2, 1364, 10.1002/pro.5560020821

Leach, 1994, Ligand docking to proteins with discrete side-chain flexibility, J Mol Biol, 235, 345, 10.1016/S0022-2836(05)80038-5

Di Nola, 1994, Molecular dynamics simulation of the docking of substrates to proteins, Proteins, 19, 174, 10.1002/prot.340190303

Luty, 1995, A molecular mechanics/grid method for evaluation of ligand—receptor interactions, J Comput Chem, 16, 454, 10.1002/jcc.540160409

Poornima, 1995, Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein—ligand interactions, J Comput Aided Mol Des, 9, 500, 10.1007/BF00124321

Wlodawer, 1994, Rational drug design: the proteinase inhibitors, Pharmacotherapy, 14, 9, 10.1002/j.1875-9114.1994.tb03627.x

Knetgel, 1994, MONTY: a Monte Carlo approach to protein—DNA recognition, J Mol Biol, 235, 318, 10.1016/S0022-2836(05)80035-X

Knetgel, 1994, Monte Carlo docking of protein—DNA complexes: incorporation of DNA flexibility and experimental data, Protein Eng, 7, 761, 10.1093/protein/7.6.761

Grootenhuis, 1994, Finding potential DNA-binding compounds by using molecular shape, J Comput Aided Mol Des, 8, 731, 10.1007/BF00124018

Prabhakar, 1994, Mechanism of DNA—drug interactions, Appl Biochem Biotechnol, 47, 39, 10.1007/BF02788674

Kubinyi, 1993

Kubinyi, 1993

Lewis, 1994, Current methods for site-directed structure generation, J Comput Aided Mol Des, 8, 467, 10.1007/BF00125381

Colman, 1994, Structure-based drug design, Curr Opin Struct Biol, 4, 868, 10.1016/0959-440X(94)90268-2

Guida, 1994, Software for structure-based drug design, Curr Opin Struct Biol, 4, 777, 10.1016/S0959-440X(94)90179-1

Kuntz, 1994, Structure-based molecular design, Accounts Chem Res, 27, 117, 10.1021/ar00041a001

Houghton, 1995

Beaudry, 1992, Directed evolution of an RNA enzyme, Science, 257, 635, 10.1126/science.1496376