Ligand binding free-energy calculations with funnel metadynamics

Ligand binding free energy and kinetics calculation in 2020

(2020) Vittorio Limongelli   Wiley Interdisciplinary Reviews-Computational Molecular Science

Understanding ligand binding selectivity in a prototypical GPCR family

(2019) Giulio Mattedi et al.   Journal of Chemical Information and Modeling

Promoting transparency and reproducibility in enhanced molecular simulations

(2019)   NATURE METHODS

Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90

(2019) Ilda D’Annessa et al.   Journal of Chemical Theory and Computation

Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor

(2018) Noureldin Saleh et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation

(2018) Arushi Prakash et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

(2018) Pim W. J. M. Frederix et al.   CHEMICAL SOCIETY REVIEWS

New developments in force fields for biomolecular simulations

(2018) Paul S Nerenberg et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Molecular Mechanism Underlying Ligand Binding to the Membrane-Embedded Site of a G-Protein-Coupled Receptor

(2018) Xiaojing Yuan et al.   Journal of Chemical Theory and Computation

A Multiscale Simulation Approach to Modelling Drug-Protein Binding Kinetics

(2018) Susanta Haldar et al.   Journal of Chemical Theory and Computation

Accelerating the Calculation of Protein–Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables

(2018) Z. Faidon Brotzakis et al.   Journal of Chemical Theory and Computation

Defining an Optimal Metric for the Path Collective Variables

(2018) Ladislav Hovan et al.   Journal of Chemical Theory and Computation

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands

(2017) Noureldin Saleh et al.   Journal of Chemical Information and Modeling

A variational conformational dynamics approach to the selection of collective variables in metadynamics

(2017) James McCarty et al.   JOURNAL OF CHEMICAL PHYSICS

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations

(2017) Rodrigo Casasnovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

(2017) Federica Moraca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites

(2016) Neal K. Broomhead et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations

(2016) Federico Comitani et al.   Journal of Chemical Theory and Computation

Computational protein–ligand docking and virtual drug screening with the AutoDock suite

(2016) Stefano Forli et al.   Nature Protocols

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase

(2016) Maria Agnese Morando et al.   Scientific Reports

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

(2015) Jim Pfaendtner et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Funnel-Metadynamics and Solution NMR to Estimate Protein–Ligand Affinities

(2015) Laura Troussicot et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics

(2014) Ya-Wen Hsiao et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic insight into ligand binding to G-quadruplex DNA

(2014) Francesco Saverio Di Leva et al.   NUCLEIC ACIDS RESEARCH

Well-Tempered Metadynamics Converges Asymptotically

(2014) James F. Dama et al.   PHYSICAL REVIEW LETTERS

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

Essential role of conformational selection in ligand binding

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

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Towards Ligand Docking Including Explicit Interface Water Molecules

(2013) Gordon Lemmon et al.   PLoS One

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

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

(2012) G. Saladino et al.   Journal of Chemical Theory and Computation

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

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

A Guide to Simple and Informative Binding Assays

(2010) Thomas D. Pollard   MOLECULAR BIOLOGY OF THE CELL

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

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

(2009) M. Bonomi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

A potential of mean force estimator based on nonequilibrium work exponential averages

(2009) Riccardo Chelli et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

(2008) Michael W. Forney et al.   PHYSICAL REVIEW E

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS