Protein–ligand binding with the coarse-grained Martini model

Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding

(2020) Tatsuki Negami et al.   CHEMICAL PHYSICS LETTERS

Baricitinib as potential treatment for 2019-nCoV acute respiratory disease

(2020) Peter Richardson et al.   LANCET

Ligand binding free energy and kinetics calculation in 2020

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

How effectively can adaptive sampling methods capture spontaneous ligand binding?

(2019) Robin Betz et al.   Journal of Chemical Theory and Computation

Investigation around the Oxadiazole Core in the Discovery of a New Chemotype of Potent and Selective FXR Antagonists

(2019) Carmen Festa et al.   ACS Medicinal Chemistry Letters

Drug–Membrane Permeability across Chemical Space

(2019) Roberto Menichetti et al.   ACS Central Science

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

(2019) Andrea Basciu et al.   Journal of Chemical Information and Modeling

Emerging Diversity in Lipid–Protein Interactions

(2019) Valentina Corradi et al.   CHEMICAL REVIEWS

Ligand Pathways in Nuclear Receptors

(2019) André Fischer et al.   Journal of Chemical Information and Modeling

Finding multiple reaction pathways of ligand unbinding

(2019) Jakub Rydzewski et al.   JOURNAL OF CHEMICAL PHYSICS

Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics

(2019) Riccardo Capelli et al.   Journal of Physical Chemistry Letters

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

(2019) Ai Niitsu et al.   Journal of Chemical Information and Modeling

Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK

(2019) Jorge Roel-Touris et al.   Journal of Chemical Theory and Computation

Pitfalls of the Martini Model

(2019) Riccardo Alessandri et al.   Journal of Chemical Theory and Computation

Molecular Mechanism of S1P Binding and Activation of the S1P1 Receptor

(2019) Zhenyan Jiang et al.   Journal of Chemical Information and Modeling

An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation

(2019) Paulo C. T. Souza et al.   Journal of Physical Chemistry Letters

Feasibility and biological rationale of repurposing sunitinib and erlotinib for dengue treatment

(2018) Szu-Yuan Pu et al.   ANTIVIRAL RESEARCH

Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways

(2018) Ariane Nunes-Alves et al.   BIOPHYSICAL JOURNAL

Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme

(2018) Jagannath Mondal et al.   PLoS Computational Biology

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3

(2018) Panagiotis I. Koukos et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview

(2018) Veronica Salmaso et al.   Frontiers in Pharmacology

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

Novel Isoxazole Derivatives with Potent FXR Agonistic Activity Prevent Acetaminophen-Induced Liver Injury

(2018) Valentina Sepe et al.   ACS Medicinal Chemistry Letters

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

(2018) Matteo Aldeghi et al.   ACS Central Science

Molecular dynamics simulations and novel drug discovery

(2017) Xuewei Liu et al.   Expert Opinion on Drug Discovery

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

(2017) James A. Graham et al.   Journal of Chemical Information and Modeling

Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins

(2017) Adolfo B. Poma et al.   Journal of Chemical Theory and Computation

The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States

(2017) James F. Dama et al.   Journal of Chemical Theory and Computation

Partitioning of caffeine in lipid bilayers reduces membrane fluidity and increases membrane thickness

(2017) Adree Khondker et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics

(2017) Yong Wang et al.   Chemical Science

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

(2017) Floris J. Van Eerden et al.   Nature Communications

Conformational modulation of the farnesoid X receptor by prenylflavonoids: Insights from hydrogen deuterium exchange mass spectrometry (HDX-MS), fluorescence titration and molecular docking studies

(2016) Liping Yang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Janus kinase inhibitors for rheumatoid arthritis

(2016) Kunihiro Yamaoka   CURRENT OPINION IN CHEMICAL BIOLOGY

Improved Side Chain Dynamics in MARTINI Simulations of Protein–Lipid Interfaces

(2016) Florian A. Herzog 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

Designer protein delivery: From natural to engineered affinity-controlled release systems

(2016) M. M. Pakulska et al.   SCIENCE

Family-wide Structural Analysis of Human Numb-Associated Protein Kinases

(2016) Fiona J. Sorrell et al.   STRUCTURE

Enantioselective Enzymes by Computational Design and In Silico Screening

(2015) Hein J. Wijma et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules

(2015) Tristan Bereau 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

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

A quantum chemical study of the ω-transaminase reaction mechanism

(2015) Karim Engelmark Cassimjee et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Src protein-tyrosine kinase structure, mechanism, and small molecule inhibitors

(2015) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Homologous ligands accommodated by discrete conformations of a buried cavity

(2015) Matthew Merski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational dynamics of human FXR-LBD ligand interactions studied by hydrogen/deuterium exchange mass spectrometry: Insights into the antagonism of the hypolipidemic agent Z-guggulsterone

(2014) Liping Yang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Adaptive resolution simulation of an atomistic protein in MARTINI water

(2014) Julija Zavadlav et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-grained molecular dynamics simulations of protein-ligand binding

(2014) Tatsuki Negami et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Design, Synthesis, and Biological Evaluation of Potent Dual Agonists of Nuclear and Membrane Bile Acid Receptors

(2014) Claudio D’Amore et al.   JOURNAL OF MEDICINAL CHEMISTRY

Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

(2014) Sam Grinter et al.   MOLECULES

Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel

(2014) C. Boiteux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Adenosine A2A Receptor as a Drug Discovery Target

(2013) Manuel de Lera Ruiz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular Mechanism of Peroxisome Proliferator-Activated Receptor α Activation by WY14643: a New Mode of Ligand Recognition and Receptor Stabilization

(2013) Amanda Bernardes et al.   JOURNAL OF MOLECULAR BIOLOGY

Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc1

(2013) Clement Arnarez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

Molecular signatures of G-protein-coupled receptors

(2013) A. J. Venkatakrishnan et al.   NATURE

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

The power of coarse graining in biomolecular simulations

(2013) Helgi I. Ingólfsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Crystal structure of the µ-opioid receptor bound to a morphinan antagonist

(2012) Aashish Manglik et al.   NATURE

Bile Acid Metabolism and the Pathogenesis of Type 2 Diabetes

(2011) Janne Prawitt et al.   Current Diabetes Reports

How Does a Drug Molecule Find Its Target Binding Site?

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

Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation

(2011) Guillaume Lebon et al.   NATURE

Obtaining fully dynamic coarse-grained models from MD

(2011) Pep Español et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine

(2011) Andrew S. Doré et al.   STRUCTURE

Structural insights into adrenergic receptor function and pharmacology

(2011) Brian K. Kobilka   TRENDS IN PHARMACOLOGICAL SCIENCES

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

(2010) A. C. M. Figueira et al.   MOLECULAR ENDOCRINOLOGY

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Use of Stabilizing Mutations To Engineer a Charged Group within a Ligand-Binding Hydrophobic Cavity in T4 Lysozyme

(2009) Lijun Liu et al.   BIOCHEMISTRY

The Role of Adenosine in Alzheimers Disease

(2009) Anisur Rahman   Current Neuropharmacology

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

(2008) Ilja V. Khavrutskii et al.   JOURNAL OF CHEMICAL PHYSICS

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