Dynamic Docking: A Paradigm Shift in Computational Drug Discovery

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

(2017) Giuseppe Deganutti et al.   Future Medicinal Chemistry

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics

(2017) S. Roy Kimura et al.   Journal of Chemical Information and Modeling

Multiscale Simulation of Receptor–Drug Association Kinetics: Application to Neuraminidase Inhibitors

(2017) Fabian Zeller et al.   Journal of Chemical Theory and Computation

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor

(2017) Gert-Jan Bekker et al.   Journal of Chemical Theory and Computation

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding

(2017) Lane W. Votapka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein–ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling

(2017) M. Bernetti et al.   MedChemComm

Recent advances in dynamic docking for drug discovery

(2017) Marco De Vivo et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations

(2016) Piero Procacci   Journal of Chemical Information and Modeling

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

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics

(2016) Phani Ghanakota et al.   JOURNAL OF MEDICINAL CHEMISTRY

Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems

(2016) Phani Ghanakota et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamic undocking and the quasi-bound state as tools for drug discovery

(2016) Sergio Ruiz-Carmona et al.   Nature Chemistry

Mapping Cholesterol Interaction Sites on Serotonin Transporter through Coarse-Grained Molecular Dynamics

(2016) Mariarosaria Ferraro et al.   PLoS One

Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme

(2016) Noelia Ferruz et al.   Scientific Reports

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

(2016) Nathaniel Stanley et al.   Scientific Reports

Protein Flexibility in Drug Discovery: From Theory to Computation

(2015) Rosa Buonfiglio et al.   ChemMedChem

Implicit solvent methods for free energy estimation

(2015) Sergio Decherchi et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Classification of Current Scoring Functions

(2015) Jie Liu et al.   Journal of Chemical Information and Modeling

Insights from Fragment Hit Binding Assays by Molecular Simulations

(2015) Noelia Ferruz et al.   Journal of Chemical Information and Modeling

Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC–MurF): experimental and computational characterization

(2015) Andrej Perdih et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Docking and Structure-Based Drug Design Strategies

(2015) Leonardo Ferreira et al.   MOLECULES

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

(2015) Robert A. Copeland   NATURE REVIEWS DRUG DISCOVERY

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

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

(2015) Lane W. Votapka et al.   PLoS Computational Biology

Markov state models of biomolecular conformational dynamics

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

Protein–Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials

(2014) Manuel P. Luitz 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

Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations

(2014) P. Bisignano et al.   Journal of Chemical Information and Modeling

Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design

(2014) Daniel Alvarez-Garcia et al.   Journal of Chemical Theory and Computation

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations

(2014) Sirish Kaushik Lakkaraju et al.   Journal of Chemical Theory and Computation

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations

(2014) S. Doerr et al.   Journal of Chemical Theory and Computation

Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

(2014) Daniel Alvarez-Garcia et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular Recognition and Ligand Association

(2013) Riccardo Baron et al.   Annual Review of Physical Chemistry

Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

(2013) Katja Ostermeir et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Exploring the role of receptor flexibility in structure-based drug discovery

(2013) Ferran Feixas et al.   BIOPHYSICAL CHEMISTRY

PLUMED 2: New feathers for an old bird

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

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

(2013) S.F. Sousa et al.   CURRENT MEDICINAL CHEMISTRY

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

(2013) E. Prabhu Raman et al.   Journal of Chemical Information and Modeling

Collecting and Assessing Human Lactate Dehydrogenase-A Conformations for Structure-Based Virtual Screening

(2013) Rosa Buonfiglio et al.   Journal of Chemical Information and Modeling

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

(2013) Ron O. Dror et al.   NATURE

A steered molecular dynamics mediated hit discovery for histone deacetylases

(2013) Subha Kalyaanamoorthy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

To milliseconds and beyond: challenges in the simulation of protein folding

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

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

(2012) Ahmet Bakan et al.   Journal of Chemical Theory and Computation

Variability in docking success rates due to dataset preparation

(2012) Christopher R. Corbeil et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure and dynamics of the M3 muscarinic acetylcholine receptor

(2012) Andrew C. Kruse et al.   NATURE

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

(2012) P. Soderhjelm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein flexibility in docking and surface mapping

(2012) Katrina W. Lexa et al.   QUARTERLY REVIEWS OF BIOPHYSICS

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

(2011) Markus A. Lill   BIOCHEMISTRY

Protein-ligand docking

(2011) Giovanni Bottegoni   Frontiers in Bioscience-Landmark

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

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

Probing theα-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis

(2010) Zuojun Guo et al.   Chemical Biology & Drug Design

Computational Approaches for Fragment-Based and De Novo Design

(2010) Kathryn Loving et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

(2010) Ian R. Craig et al.   Journal of Chemical Information and Modeling

A Note on the Standard State’s Binding Free Energy

(2010) Ignacio J. General   Journal of Chemical Theory and Computation

Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors

(2010) Francesco Colizzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping

(2010) Katrina W. Lexa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2010) Vijay S. Pande et al.   METHODS

Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics

(2009) Davide Provasi et al.   BIOCHEMISTRY

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics

(2009) Matteo Masetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

(2009) Olgun Guvench et al.   PLoS Computational Biology

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Electrostatic funneling of substrate in mitochondrial inner membrane carriers

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

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

Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies

(2007) Matteo Masetti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY