Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations

Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket

(2023) Jinan Wang et al.   Journal of Chemical Theory and Computation

DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling

(2023) Anupam Anand Ojha et al.   Journal of Chemical Theory and Computation

Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases**

(2022) Mrinal Shekhar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine

(2022) Lane W. Votapka et al.   Journal of Chemical Information and Modeling

Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective

(2022) Katya Ahmad et al.   Frontiers in Molecular Biosciences

Simulation of ligand dissociation kinetics from the protein kinase PYK2

(2022) Justin Spiriti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Gaussian accelerated molecular dynamics: Principles and applications

(2021) Jinan Wang et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling

(2021) Surl-Hee Ahn et al.   Journal of Chemical Theory and Computation

The role of JAK/STAT signaling pathway and its inhibitors in diseases

(2020) Ping Xin et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

Correlating Drug–Target Residence Time and Post-antibiotic Effect: Insight into Target Vulnerability

(2020) Shabnam Davoodi et al.   ACS Infectious Diseases

Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach

(2020) Benjamin R. Jagger et al.   Journal of Chemical Theory and Computation

Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics

(2020) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Kinetics of Drug Binding and Residence Time

(2019) Mattia Bernetti et al.   Annual Review of Physical Chemistry

Baricitinib: The Second FDA-Approved JAK Inhibitor for the Treatment of Rheumatoid Arthritis

(2019) Amanda Mogul et al.   ANNALS OF PHARMACOTHERAPY

Pharmacokinetic–pharmacodynamic models that incorporate drug–target binding kinetics

(2019) Fereidoon Daryaee et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Investigating Drug–Target Residence Time in Kinases through Enhanced Sampling Simulations

(2019) Dorothea Gobbo et al.   Journal of Chemical Theory and Computation

An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes

(2019) Mattia Bernetti et al.   Journal of Chemical Theory and Computation

Estimation of Protein–Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations

(2019) Steffen Wolf et al.   Journal of Chemical Information and Modeling

Computational Analysis of Kinase Inhibitor Selectivity using Structural Knowledge

(2018) Yu-Chen Lo et al.   BIOINFORMATICS

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

(2018) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Mechanistic Insights into Regulation of JAK2 Tyrosine Kinase

(2018) Stevan R. Hubbard   Frontiers in Endocrinology

Multiscale methods in drug design bridge chemical and biological complexity in the search for cures

(2018) Rommie E. Amaro et al.   Nature Reviews Chemistry

The molecular details of cytokine signalling via the JAK/STAT pathway

(2018) Rhiannon Morris et al.   PROTEIN SCIENCE

Suitability of MMGBSA for the selection of correct ligand binding modes from docking results

(2018) Mira Ahinko et al.   Chemical Biology & Drug Design

Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase

(2018) Leela S. Dodda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

POVME 3.0: Software for Mapping Binding Pocket Flexibility

(2017) Jeffrey R. Wagner 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

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

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

JAK inhibition as a therapeutic strategy for immune and inflammatory diseases

(2017) Daniella M. Schwartz et al.   NATURE REVIEWS DRUG DISCOVERY

A new paradigm for atomically detailed simulations of kinetics in biophysical systems

(2017) Ron Elber   QUARTERLY REVIEWS OF BIOPHYSICS

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

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

How and when does an anticancer drug leave its binding site?

(2017) Pratyush Tiwary et al.   Science Advances

JAK inhibition using tofacitinib for inflammatory bowel disease treatment: a hub for multiple inflammatory cytokines

(2016) Silvio Danese et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Genetic basis and molecular pathophysiology of classical myeloproliferative neoplasms

(2016) William Vainchenker et al.   BLOOD

Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations

(2016) Anthony J. Clark et al.   Journal of Chemical Theory and Computation

Biophysics in drug discovery: impact, challenges and opportunities

(2016) Jean-Paul Renaud et al.   NATURE REVIEWS DRUG DISCOVERY

The JAK-STAT Pathway: Impact on Human Disease and Therapeutic Intervention

(2015) John J. O'Shea et al.   Annual Review of Medicine

Enhanced sampling techniques in molecular dynamics simulations of biological systems

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

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

(2015) Rodrigo Galindo-Murillo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis

(2015) Matthew C. Zwier et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

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

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

(2015) Nuria Plattner et al.   Nature Communications

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

(2015) Huiyong Sun et al.   Scientific Reports

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

(2015) Luca Mollica et al.   Scientific Reports

Tofacitinib

(2014) Deepti Vyas et al.   ANNALS OF PHARMACOTHERAPY

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

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force

(2014) Hugh S. C. Martin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

(2014) Jeffrey Comer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the absence of intrahelical DNA dynamics on the μs to ms timescale

(2014) Rodrigo Galindo-Murillo et al.   Nature Communications

Janus kinase inhibitors in autoimmune diseases

(2013) John J O'Shea et al.   ANNALS OF THE RHEUMATIC DISEASES

Strategic use of conformational bias and structure based design to identify potent JAK3 inhibitors with improved selectivity against the JAK family and the kinome

(2013) Stephen M. Lynch et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Discovery of novel Jak2–Stat pathway inhibitors with extended residence time on target

(2013) Huiping Guan et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Measuring and comparing structural fluctuation patterns in large protein datasets

(2012) Edvin Fuglebakk et al.   BIOINFORMATICS

Ligand–receptor interaction platforms and their applications for drug discovery

(2012) Ye Fang   Expert Opinion on Drug Discovery

Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges

(2012) Ejaz Ahmad et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

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

Heterodimeric JAK–STAT activation as a mechanism of persistence to JAK2 inhibitor therapy

(2012) Priya Koppikar et al.   NATURE

A Double-Blind, Placebo-Controlled Trial of Ruxolitinib for Myelofibrosis

(2012) Srdan Verstovsek et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tofacitinib, an Oral Janus Kinase Inhibitor, in Active Ulcerative Colitis

(2012) William J. Sandborn et al.   NEW ENGLAND JOURNAL OF MEDICINE

An overview of the Amber biomolecular simulation package

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

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Phase IIb dose-ranging study of the oral JAK inhibitor tofacitinib (CP-690,550) or adalimumab monotherapy versus placebo in patients with active rheumatoid arthritis with an inadequate response to disease-modifying antirheumatic drugs

(2011) Roy Fleischmann et al.   ARTHRITIS AND RHEUMATISM

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Modulation of Innate and Adaptive Immune Responses by Tofacitinib (CP-690,550)

(2011) Kamran Ghoreschi et al.   JOURNAL OF IMMUNOLOGY

Umbrella sampling

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

Metadynamics

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

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Browndye: A software package for Brownian dynamics

(2010) Gary A. Huber et al.   COMPUTER PHYSICS COMMUNICATIONS

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Drug–target residence time: critical information for lead optimization

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

Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6

(2010) Jill E. Chrencik et al.   JOURNAL OF MOLECULAR BIOLOGY

POVME: An algorithm for measuring binding-pocket volumes

(2010) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Janus kinases in immune cell signaling

(2009) Kamran Ghoreschi et al.   IMMUNOLOGICAL REVIEWS

Markovian milestoning with Voronoi tessellations

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

(2009) Slimane Doudou et al.   Journal of Chemical Theory and Computation

Dissecting Specificity in the Janus Kinases: The Structures of JAK-Specific Inhibitors Complexed to the JAK1 and JAK2 Protein Tyrosine Kinase Domains

(2009) Neal K. Williams et al.   JOURNAL OF MOLECULAR BIOLOGY

Membrane proteins: molecular dynamics simulations

(2008) E LINDAHL et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Long-time convergence of an adaptive biasing force method

(2008) Tony Lelièvre et al.   NONLINEARITY