Receptor flexibility in small-molecule docking calculations

Algorithm improvements for molecular dynamics simulations

(2011) Per Larsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Ensemble Docking from Homology Models

(2010) Eva Maria Novoa et al.   Journal of Chemical Theory and Computation

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

(2010) D. D. Boehr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible ligand docking using conformational ensembles

(2010) David M. Lorber et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

(2010) Daniel Seeliger et al.   PLoS Computational Biology

Simplified Computational Methods for the Analysis of Protein Flexibility

(2009) Igor Kuznetsov   CURRENT PROTEIN & PEPTIDE SCIENCE

Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization

(2009) Janet L. Paulsen et al.   Journal of Chemical Information and Modeling

Evaluating Docking Methods for Prediction of Binding Affinities of Small Molecules to the G ProteinβγSubunits

(2009) Min-Sun Park et al.   Journal of Chemical Information and Modeling

Molecular Docking Screens Using Comparative Models of Proteins

(2009) Hao Fan et al.   Journal of Chemical Information and Modeling

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Conformational selection or induced fit: A flux description of reaction mechanism

(2009) G. G. Hammes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors

(2008) Christopher R. Corbeil et al.   Journal of Chemical Information and Modeling

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

(2008) Giovanni Bottegoni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening

(2008) Daria B. Kokh et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins†

(2008) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis

(2008) Thomas R. Weikl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking

(2008) Erin S. D. Bolstad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking

(2008) Erin S. D. Bolstad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MADAMM: A multistaged docking with an automated molecular modeling protocol

(2008) N. M. F. S. A. Cerqueira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

(2007) N Moitessier et al.   BRITISH JOURNAL OF PHARMACOLOGY

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

(2007) Mark A. Olson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational selectionin silico: Loop latching motions and ligand binding in enzymes

(2007) Sergio Wong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS