A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

Comparison of simple potential functions for simulating liquid water

1983 • 37,746 citations

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1977 • 19,896 citations

General atomic and molecular electronic structure system

1993 • 19,663 citations

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

1983 • 14,615 citations

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

1993 • 7,156 citations

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

2000 • 3,794 citations

Essential dynamics of proteins

1993 • 3,179 citations

A Fast Flexible Docking Method using an Incremental Construction Algorithm

1996 • 2,706 citations

A geometric approach to macromolecule-ligand interactions

1982 • 2,146 citations

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

1996 • 1,600 citations

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

1995 • 1,514 citations

Automated docking of substrates to proteins by simulated annealing

1990 • 1,193 citations

Conserved Folding in Retroviral Proteases: Crystal Structure of Synthetic HIV-1 Protease

1989 • 1,155 citations

<scp>AMBER</scp>: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

1981 • 1,120 citations

Conformational change of proteins arising from normal mode calculations

2001 • 874 citations

Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization

1972 • 736 citations

Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme

1985 • 718 citations

Structure of Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 Å Resolution

1989 • 683 citations

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

1995 • 667 citations

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution

1992 • 502 citations

Building-block approach for determining low-frequency normal modes of macromolecules

2000 • 477 citations

Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

2001 • 460 citations

FlexE: efficient molecular docking considering protein structure variations

2001 • 430 citations

Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

2004 • 413 citations

“Soft docking”: Matching of molecular surface cubes

1991 • 402 citations

Flexible protein–ligand docking by global energy optimization in internal coordinates

1997 • 397 citations

The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

1991 • 387 citations

Molecular docking to ensembles of protein structures 1 1Edited by B. Honig

1997 • 380 citations

Ligand docking to proteins with discrete side-chain flexibility

1994 • 358 citations

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

2003 • 351 citations

Side-chain flexibility in proteins upon ligand binding

2000 • 289 citations

Flexible ligand docking using a genetic algorithm

1995 • 269 citations

The isothermal/isobaric molecular dynamics ensemble

1983 • 207 citations

Collective Motions in HIV-1 Reverse Transcriptase: Examination of Flexibility and Enzyme Function

1999 • 206 citations

The Mechanism and Pathway of pH Induced Swelling in Cowpea Chlorotic Mottle Virus

2002 • 205 citations

Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the β1,4-galactosyltransferase-I11Edited by R. Huber

2001 • 194 citations

The essential dynamics of thermolysin: Confirmation of the hinge‐bending motion and comparison of simulations in vacuum and water

1995 • 191 citations

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

1995 • 162 citations

The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking

2003 • 138 citations

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

1999 • 128 citations

Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers

1998 • 120 citations

Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies

1994 • 98 citations

Molecular dynamics simulation of the docking of substrates to proteins

1994 • 94 citations

Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion

1990 • 90 citations

Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation

1997 • 84 citations

A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening

2000 • 84 citations

Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP

2004 • 84 citations

Dipped adcluster model for chemisorptions and catalytic reactions on a metal surface

1987 • 71 citations

Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex

1999 • 65 citations

Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors

2004 • 49 citations

Computer simulations of ligand-protein binding with ensembles of protein conformations: A Monte Carlo study of HIV-1 protease binding energy landscapes

1999 • 47 citations

Dipped adcluster model for chemisorptions and catalytic reactions on a metal surface: Image force correction and applications to Pd–O2 adclusters

1991 • 42 citations

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding.

1996 • 39 citations

Docking macromolecules with flexible segments

2003 • 34 citations

Ligand-induced Conformational Changes and a Mechanism for Domain Closure in Aspergillus nidulans Dehydroquinate Synthase

2003 • 22 citations

Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A

1997 • 17 citations

Correlation between normal modes in the 20–200 cm−1 frequency range and localized torsion motions related to certain collective motions in proteins

2002 • 6 citations