Flexible receptor docking for drug discovery

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

(2015) Urmi Doshi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

(2015) Junichi Higo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Reduction of False Positives in Structure-Based Virtual Screening When Receptor Plasticity Is Considered

(2015) Yaw Awuni et al.   MOLECULES

Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors

(2015) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

(2015) Sergio Decherchi et al.   Nature Communications

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

(2014) Andrea Cavalli et al.   ACCOUNTS OF CHEMICAL RESEARCH

A study of the molecular mechanism of binding kinetics and long residence times of human CCR5 receptor small molecule allosteric ligands

(2014) David C Swinney et al.   BRITISH JOURNAL OF PHARMACOLOGY

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Multi-Conformer Ensemble Docking to Difficult Protein Targets

(2014) Sally R. Ellingson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular simulation of drug-binding kinetics

(2014) Chung F. Wong   MOLECULAR SIMULATION

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

(2014) N. Greives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hardware support for fine-grained event-driven computation in Anton 2

(2013) J. P. Grossman et al.   ACM SIGPLAN NOTICES

Conformational Selection Is a Dominant Mechanism of Ligand Binding

(2013) Austin D. Vogt et al.   BIOCHEMISTRY

Interplay between conformational selection and induced fit in multidomain protein–ligand binding probed by paramagnetic relaxation enhancement

(2013) G. Marius Clore   BIOPHYSICAL CHEMISTRY

Essential role of conformational selection in ligand binding

(2013) Austin D. Vogt et al.   BIOPHYSICAL CHEMISTRY

Drug Design for Protein Kinases and Phosphatases: Flexible-Receptor Docking, Binding Affinity and Specificity, and Drug-Binding Kinetics

(2013) Chung Wong et al.   CURRENT PHARMACEUTICAL DESIGN

Simulation reveals two major docking pathways between the hexapeptide GDYMNM and the catalytic domain of the insulin receptor protein kinase

(2013) Zunnan Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein dynamics and conformational selection in bidirectional signal transduction

(2012) Ruth Nussinov et al.   BMC BIOLOGY

Dynamics and mechanisms of coupled protein folding and binding reactions

(2012) Thomas Kiefhaber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols

(2012) David J. Osguthorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease

(2012) Simon Leis et al.   PLoS One

Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein

(2011) Denis Bucher et al.   BIOCHEMISTRY

Conformational adaptation in drug–target interactions and residence time

(2011) Robert A Copeland   Future Medicinal Chemistry

Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation

(2011) Ron Dror et al.   IEEE MICRO

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

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

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

(2011) Giovanni Bottegoni et al.   PLoS One

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

Conformational Selection in G-Proteins: Lessons from Ras and Rho

(2010) Barry J. Grant et al.   BIOPHYSICAL JOURNAL

Reaching biological timescales with all-atom molecular dynamics simulations

(2010) Matthew C Zwier et al.   CURRENT OPINION IN PHARMACOLOGY

Emerging Methods for Ensemble-Based Virtual Screening

(2010) Rommie Amaro et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Predicting the accuracy of protein-ligand docking on homology models

(2010) Annalisa Bordogna et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition

(2010) Michael D. Daily et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamic Ligand-Induced-Fit Simulation via Enhanced Conformational Samplings and Ensemble Dockings: A Survivin Example

(2010) In-Hee Park et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Flexible ligand docking using conformational ensembles

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

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

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

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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

Beyond Thermodynamics: Drug Binding Kinetics Could Influence Epidermal Growth Factor Signaling

(2009) Mayank Goyal et al.   JOURNAL OF MEDICINAL CHEMISTRY

Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems

(2009) Zunnan Huang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Erratum: The role of dynamic conformational ensembles in biomolecular recognition

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

The role of dynamic conformational ensembles in biomolecular recognition

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

Residence Time of Receptor−Ligand Complexes and Its Effect on Biological Function

(2008) Peter J. Tummino et al.   BIOCHEMISTRY

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Flexible ligand docking to multiple receptor conformations: a practical alternative

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

Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking

(2008) Zunnan Huang et al.   JOURNAL OF COMPUTATIONAL 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

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

(2008) S. M. Sullivan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible protein–flexible ligand docking with disrupted velocity simulated annealing

(2007) Zunnan Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS