Accounting for global protein deformability during protein–protein and protein–ligand docking

Essential dynamics of proteins

1993 • 3,179 citations

Comparative Protein Structure Modeling of Genes and Genomes

2000 • 3,120 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

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

1997 • 1,344 citations

Principles of docking: An overview of search algorithms and a guide to scoring functions

2002 • 1,200 citations

Regulation of Protein Kinases

2004 • 1,103 citations

Conformational change of proteins arising from normal mode calculations

2001 • 874 citations

Molecular Recognition and Docking Algorithms

2003 • 762 citations

Analysis of domain motions by approximate normal mode calculations

1998 • 711 citations

Implications of protein flexibility for drug discovery

2003 • 700 citations

Atomic Structure of FKBP-FK506, an Immunophilin-Immunosuppressant Complex

1991 • 641 citations

A review of protein-small molecule docking methods.

2002 • 633 citations

Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats

1993 • 614 citations

Issues and progress with protein kinase inhibitors for cancer treatment

2003 • 529 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

Principal Component Analysis and Long Time Protein Dynamics

1996 • 398 citations

Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme

2002 • 385 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

High-throughput docking for lead generation

2001 • 337 citations

Protein–protein docking with a reduced protein model accounting for side‐chain flexibility

2003 • 332 citations

Accommodating protein flexibility in computational drug design.

2000 • 321 citations

Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis

1999 • 320 citations

PKA: a portrait of protein kinase dynamics

2003 • 304 citations

Solution Structure of FKBP, a Rotamase Enzyme and Receptor for FK506 and Rapamycin

1991 • 302 citations

Side-chain flexibility in proteins upon ligand binding

2000 • 289 citations

Deciphering common failures in molecular docking of ligand-protein complexes.

2000 • 217 citations

Mechanism of Ribonuclease Inhibition by Ribonuclease Inhibitor Protein Based on the Crystal Structure of its Complex with Ribonuclease A

1996 • 208 citations

The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking

2005 • 167 citations

Molecular docking using surface complementarity

1996 • 161 citations

The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase.

1999 • 159 citations

Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential

1997 • 150 citations

Dynamic Features of cAMP-dependent Protein Kinase Revealed by Apoenzyme Crystal Structure

2003 • 134 citations

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

1999 • 128 citations

Docking small ligands in flexible binding sites

1998 • 128 citations

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

1998 • 120 citations

Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design

1999 • 113 citations

Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin

1995 • 113 citations

Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase

2001 • 91 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

Molecular docking using surface complementarity

1996 • 84 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

A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility

1998 • 64 citations

Protein Flexibility and Computer-Aided Drug Design

2003 • 61 citations

Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems

1999 • 58 citations

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

2004 • 53 citations

Docking macromolecules with flexible segments

2003 • 34 citations

Refinement of protein cores and protein–peptide interfaces using a potential scaling approach

2005 • 19 citations

The role of structure in kinase-targeted inhibitor design.

2004 • 15 citations

The Protein Kinase Resource: everything you always wanted to know about protein kinases but were afraid to ask

2005 • 14 citations