Virtual screening—an overview

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

1997 • 6,184 citations

Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

1988 • 3,852 citations

Semianalytical treatment of solvation for molecular mechanics and dynamics

1990 • 3,585 citations

A Fast Flexible Docking Method using an Incremental Construction Algorithm

1996 • 2,706 citations

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

1985 • 2,597 citations

Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models

1994 • 2,072 citations

Free energy calculations: Applications to chemical and biochemical phenomena

1993 • 2,045 citations

The Properties of Known Drugs. 1. Molecular Frameworks

1996 • 2,042 citations

Hydrogen bonding in globular proteins

1984 • 1,760 citations

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

1995 • 1,514 citations

Tertiary templates for proteins

1987 • 1,485 citations

Applications of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries

1994 • 1,130 citations

Applications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future Directions

1994 • 1,126 citations

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

1996 • 1,005 citations

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

1994 • 975 citations

Atom pairs as molecular features in structure-activity studies: definition and applications

1985 • 952 citations

The computer program LUDI: A new method for the de novo design of enzyme inhibitors

1992 • 821 citations

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

1995 • 667 citations

Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection

1996 • 625 citations

Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

1996 • 585 citations

Functionality maps of binding sites: A multiple copy simultaneous search method

1991 • 535 citations

Atomic solvation parameters applied to molecular dynamics of proteins in solution

1992 • 527 citations

From atoms and bonds to three-dimensional atomic coordinates: automatic model builders

1993 • 408 citations

Structure and Mechanism of Inosine Monophosphate Dehydrogenase in Complex with the Immunosuppressant Mycophenolic Acid

1996 • 406 citations

The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding

1997 • 372 citations

Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes

1995 • 345 citations

Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors

1987 • 326 citations

HINT: A new method of empirical hydrophobic field calculation for CoMFA

1991 • 325 citations

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

1989 • 319 citations

Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery

1995 • 299 citations

FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure

1994 • 271 citations

Flexible ligand docking using a genetic algorithm

1995 • 269 citations

The combinatorial synthesis and chemical and biological evaluation of a 1,4-benzodiazepine library.

1994 • 265 citations

An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations

1993 • 264 citations

Chemical Similarity Using Physiochemical Property Descriptors

1996 • 261 citations

SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence

1996 • 257 citations

Docking flexible ligands to macromolecular receptors by molecular shape

1986 • 241 citations

VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands

1996 • 233 citations

A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site

1995 • 224 citations

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

1993 • 221 citations

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase

1993 • 206 citations

Matching chemistry and shape in molecular docking

1993 • 205 citations

Optimization of the Biological Activity of Combinatorial Compound Libraries by a Genetic Algorithm

1995 • 197 citations

Analysis of Conformational Coverage. 1. Validation and Estimation of Coverage

1995 • 190 citations

ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures

1989 • 188 citations

Multiple Highly Diverse Structures Complementary to Enzyme Binding Sites: Results of Extensive Application of a de Novo Design Method Incorporating Combinatorial Growth

1994 • 183 citations

Topological Approach to Drug Design

1995 • 182 citations

Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions

1995 • 180 citations

Using a Genetic Algorithm To Suggest Combinatorial Libraries

1995 • 178 citations

SPROUT: Recent developments in the de novo design of molecules

1994 • 168 citations

A molecular mechanics/grid method for evaluation of ligand–receptor interactions

1995 • 162 citations

Receptor Surface Models. 1. Definition and Construction

1995 • 160 citations

Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D

1997 • 152 citations

Evolutionary algorithms in computer-aided molecular design

1996 • 146 citations

The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries

1997 • 142 citations

A good ligand is hard to find: Automated docking methods

1993 • 136 citations

SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility

1995 • 128 citations

A Fast Algorithm For Selecting Sets Of Dissimilar Molecules From Large Chemical Databases

1995 • 128 citations

Automated chemical hypothesis generation and database searching with Catalyst®

1995 • 119 citations

Flexibases: A way to enhance the use of molecular docking methods

1994 • 115 citations

Genetic algorithms in molecular recognition and design

1995 • 112 citations

Flexible ligand docking without parameter adjustment across four ligand–receptor complexes

1995 • 112 citations

Molecular Diversity in Chemical Databases: Comparison of Medicinal Chemistry Knowledge Bases and Databases of Commercially Available Compounds

1996 • 110 citations

Application of Genetic Algorithms to Combinatorial Synthesis: A Computational Approach to Lead Identification and Lead Optimization^,

1996 • 107 citations

Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces

1989 • 105 citations

Ordered water in macromolecular structure

1994 • 100 citations

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

1995 • 97 citations

Docking small-molecule ligands into active sites

1995 • 97 citations

A paradigm for drug discovery employing encoded combinatorial libraries.

1995 • 92 citations

Energetic and Entropic Factors Determining Binding Affinity in Protein-Ligand Complexes

1997 • 91 citations

An automated method for dynamic ligand design

1995 • 89 citations

Hydration in drug design. 2. Influence of local site surface shape on water binding

1995 • 87 citations

A fast and efficient method for 2D and 3D molecular shape description

1992 • 86 citations

WIZARD: AI in conformational analysis

1987 • 76 citations

PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology.

1997 • 70 citations

Parallel-compound synthesis: Methodology for accelerating drug discovery

1996 • 66 citations

Encoded combinatorial chemistry: Synthesis and screening of a library of highly functionalized pyrrolidines

1997 • 65 citations

New molecular shape descriptors: Application in database screening

1995 • 61 citations

Docking flexible molecules: A case study of three proteins

1995 • 59 citations

Searching for pharmacophores in large coordinate data bases and its use in drug design.

1989 • 58 citations

Conformational searching methods for small molecules. I. Study of the sybyl search method

1993 • 42 citations

The measurement of molecular diversity: A three-dimensional approach

1996 • 42 citations

Similarity searching in files of three-dimensional chemical structures: representation and searching of molecular electrostatic potentials using field-graphs.

1997 • 41 citations

Evolutionary and genetic methods in drug design

1996 • 34 citations

AIMB: Analogy and intelligence in model building. System description and performance characteristics

1988 • 31 citations

Automated conformational analysis: Algorithms for the efficient construction of low-energy conformations

1990 • 24 citations

PRO_LIGAND: An Approach to de Novo Molecular Design. 5. Tools for the Analysis of Generated Structures

1995 • 23 citations

Conformational searching methods for small molecules. III. Study of stochastic methods available in SYBYL and MACROMODEL

1996 • 22 citations

Computational screening of combinatorial libraries

1996 • 21 citations

The Application of Neural Networks in Conformational Analysis. 1. Prediction of Minimum and Maximum Interatomic Distances

1995 • 13 citations

An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility

1996 • 12 citations

Design considerations and computer modeling related to the development of molecular scaffolds and peptide mimetics for combinatorial chemistry

1996 • 8 citations

Computerized Chemical Data Standards: Databases, Data Interchange, and Information Systems

1994 • 6 citations