Modeling loop backbone flexibility in receptor-ligand docking simulations

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

(2011) Markus A. Lill   BIOCHEMISTRY

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking*

(2011) Simon Leis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions

(2011) Bin Lin et al.   Journal of Physical Chemistry Letters

Receptor flexibility in small-molecule docking calculations

(2011) Daria B. Kokh et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

(2010) Thomas Steinbrecher et al.   CURRENT MEDICINAL CHEMISTRY

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

2009 FDA drug approvals

(2010) Bethan Hughes   NATURE REVIEWS DRUG DISCOVERY

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

Flexibility and inhibitor binding in cdc25 phosphatases

(2010) Guilherme Menegon Arantes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Managing protein flexibility in docking and its applications

(2009) Chandrika B-Rao et al.   DRUG DISCOVERY TODAY

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

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

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

(2009) Roger S. Armen et al.   Journal of Chemical Theory and Computation

Selectively Nonselective Kinase Inhibition: Striking the Right Balance

(2009) Richard Morphy   JOURNAL OF MEDICINAL CHEMISTRY

Three amino acids in the D2dopamine receptor regulate selective ligand function and affinity

(2009) David F. Cummings et al.   JOURNAL OF NEUROCHEMISTRY

The role of dynamic conformational ensembles in biomolecular recognition

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

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

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

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

(2008) Anthony K. Felts et al.   Journal of Chemical Theory and Computation

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

(2008) Sidhartha Chaudhury et al.   JOURNAL OF MOLECULAR BIOLOGY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

A conserved protonation-dependent switch controls drug binding in the Abl kinase

(2008) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Toward better refinement of comparative models: Predicting loops in inexact environments

(2008) Benjamin D. Sellers et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling and Selection of Flexible Proteins for Structure-Based Drug Design: Backbone and Side Chain Movements in p38 MAPK

(2007) Jyothi Subramanian et al.   ChemMedChem