Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies

Investigation of α-conotoxin unbinding using umbrella sampling

(2016) Rilei Yu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Computational study on the binding and unbinding mechanism of HCV NS5B with the inhibitor GS-461203 and substrate using conventional and steered molecular dynamics simulations

(2016) Dabo Pan et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Impact, determination and prediction of drug–receptor residence times for GPCRs

(2016) Christofer S Tautermann   CURRENT OPINION IN PHARMACOLOGY

Water, water, everywhere… It's time to stop and think

(2016) Michael S. Bodnarchuk   DRUG DISCOVERY TODAY

Can residence time offer a useful strategy to target agonist drugs for sustained GPCR responses?

(2016) J. Daniel Hothersall et al.   DRUG DISCOVERY TODAY

Deciphering the Complexity of Ligand–Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations

(2016) Alberto Cuzzolin et al.   Journal of Chemical Information and Modeling

How wet should be the reaction coordinate for ligand unbinding?

(2016) Pratyush Tiwary et al.   JOURNAL OF CHEMICAL PHYSICS

Predicting bioactive conformations and binding modes of macrocycles

(2016) Andrew Anighoro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein–Ligand Residence Times

(2016) Luca Mollica et al.   JOURNAL OF MEDICINAL CHEMISTRY

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position

(2016) Kevin W. Kastner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Stacking with No Planarity?

(2016) Hakan Gunaydin et al.   ACS Medicinal Chemistry Letters

The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor

(2016) Nathaniel Stanley et al.   Scientific Reports

Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000

(2015) Giuseppe Deganutti et al.   BIOORGANIC & MEDICINAL CHEMISTRY

An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512

(2015) Giulia Palermo et al.   CHEMICAL COMMUNICATIONS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Decoding the Role of Water Dynamics in Ligand–Protein Unbinding: CRF1R as a Test Case

(2015) Andrea Bortolato et al.   Journal of Chemical Information and Modeling

Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

(2015) Stefan Geschwindner et al.   JOURNAL OF MEDICINAL CHEMISTRY

The drug–target residence time model: a 10-year retrospective

(2015) Robert A. Copeland   NATURE REVIEWS DRUG DISCOVERY

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

(2015) Kalli Kappel et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Exploring the recognition pathway at the human A2A adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations

(2015) Davide Sabbadin et al.   MedChemComm

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

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

(2015) Sergio Decherchi et al.   Nature Communications

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

(2015) Luca Mollica et al.   Scientific Reports

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5

(2014) Jagdish Suresh Patel et al.   Journal of Chemical Information and Modeling

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

(2014) Matteo Salvalaglio et al.   Journal of Chemical Theory and Computation

Optimization of Potent DFG-in Inhibitors of Platelet Derived Growth Factor Receptorβ (PDGF-Rβ) Guided by Water Thermodynamics

(2014) Rebecca Horbert et al.   JOURNAL OF MEDICINAL CHEMISTRY

A fundamental view of enthalpy–entropy compensation

(2014) Ulf Ryde   MedChemComm

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

(2014) Shuo Gu et al.   PLoS Computational Biology

Profound Methyl Effects in Drug Discovery and a Call for New CH Methylation Reactions

(2013) Heike Schönherr et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Essential role of conformational selection in ligand binding

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

Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine

(2013) David E. Shaw   BIOPHYSICAL JOURNAL

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

Pharmacokinetics and the drug–target residence time concept

(2013) Göran Dahl et al.   DRUG DISCOVERY TODAY

Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study

(2013) Andrea Bortolato et al.   Journal of Chemical Information and Modeling

Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR–Ligand Recognition: The Human A2A Adenosine Receptor as a Key Study

(2013) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions

(2013) Weihong Zhang et al.   Journal of Chemical Theory and Computation

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

(2013) Kai Wang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Population Based Reweighting of Scaled Molecular Dynamics

(2013) William Sinko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding

(2013) Benjamin Breiten et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism

(2012) Austin D. Vogt et al.   BIOCHEMISTRY

Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions

(2012) Kim D. Collins   BIOPHYSICAL CHEMISTRY

Towards the prediction of order parameters from molecular dynamics simulations in proteins

(2012) Juan R. Perilla et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

Methyl Effects on Protein–Ligand Binding

(2012) Cheryl S. Leung et al.   JOURNAL OF MEDICINAL CHEMISTRY

Clozapine, atypical antipsychotics, and the benefits of fast-off D2 dopamine receptor antagonism

(2012) Georges Vauquelin et al.   NAUNYN-SCHMIEDEBERGS ARCHIVES OF PHARMACOLOGY

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

(2012) Gregory A. Ross et al.   PLoS One

Sampling protein motion and solvent effect during ligand binding

(2012) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aromatic Rings in Chemical and Biological Recognition: Energetics and Structures

(2011) Laura M. Salonen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Calculating kinetics and pathways of protein–ligand association

(2011) Martin Held et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design

(2011) Peter Schmidtke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Substrate Binding Process and Mechanistic Functioning of Type 1 11β-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods

(2011) Angelo D. Favia et al.   PLoS One

Pathway and mechanism of drug binding to G-protein-coupled receptors

(2011) Ron O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics of Ligand Binding and Efficiency

(2011) Charles H. Reynolds et al.   ACS Medicinal Chemistry Letters

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Ligand binding assays at equilibrium: validation and interpretation

(2010) Edward C. Hulme et al.   BRITISH JOURNAL OF PHARMACOLOGY

Drug–target residence time: critical information for lead optimization

(2010) Hao Lu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The Role of Water Molecules in Computational Drug Design

(2010) Stephanie de Beer et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

(2010) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor

(2010) Christopher Higgs et al.   ACS Medicinal Chemistry Letters

Calculation of Proteins’ Total Side-Chain Torsional Entropy and Its Influence on Protein–Ligand Interactions

(2009) Kateri H. DuBay et al.   JOURNAL OF MOLECULAR BIOLOGY

Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations

(2009) Fabio Pietrucci et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

(2009) Pavel Banáš et al.   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

Multiscale methods for macromolecular simulations

(2008) Paul Sherwood et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations

(2008) Mikael Peräkylä   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Beyond Induced-Fit Receptor-Ligand Interactions: Structural Changes that Can Significantly Extend Bond Lifetimes

(2008) Lina M. Nilsson et al.   STRUCTURE

Water as an Active Constituent in Cell Biology

(2007) Philip Ball   CHEMICAL REVIEWS

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

(2007) Nikola Trbovic et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS