P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy

(2014) Kilian V. M. Huber et al.   NATURE

Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia

(2013) Erich Piovan et al.   CANCER CELL

Molecular Pathways: ROS1 Fusion Proteins in Cancer

(2013) K. D. Davies et al.   CLINICAL CANCER RESEARCH

Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy

(2013) Hui-Yong Sun et al.   Journal of Chemical Information and Modeling

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches

(2013) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches

(2013) Peichen Pan et al.   Journal of Chemical Information and Modeling

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

(2013) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations

(2013) Fabian Zeller et al.   Journal of Chemical Theory and Computation

Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding

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

Ligand-Dependent Activation and Deactivation of the Human Adenosine A2A Receptor

(2013) Jianing Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases

(2013) Yen-Lin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recovery from slow inactivation in K+ channels is controlled by water molecules

(2013) Jared Ostmeyer et al.   NATURE

Tumor adaptation and resistance to RAF inhibitors

(2013) Piro Lito et al.   NATURE MEDICINE

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Acquired Resistance to Crizotinib from a Mutation in CD74–ROS1

(2013) Mark M. Awad et al.   NEW ENGLAND JOURNAL OF MEDICINE

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

(2013) Fang Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two-state dynamics of the SH3–SH2 tandem of Abl kinase and the allosteric role of the N-cap

(2013) Carles Corbi-Verge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvent fluctuations in hydrophobic cavity–ligand binding kinetics

(2013) Piotr Setny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

(2013) Y.-L. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

(2013) L. Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The allosteric communication pathways in KIX domain of CBP

(2013) F. Palazzesi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Free-energy landscape of protein oligomerization from atomistic simulations

(2013) A. Barducci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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 pore of voltage-gated potassium ion channels is strained when closed

(2013) Philip W. Fowler et al.   Nature Communications

A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

(2012) Hui-Yong Sun et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

(2012) Mary Hongying Cheng et al.   BIOPHYSICAL JOURNAL

The ALKF1174L Mutation Potentiates the Oncogenic Activity of MYCN in Neuroblastoma

(2012) Teeara Berry et al.   CANCER CELL

Identifying and Targeting ROS1 Gene Fusions in Non-Small Cell Lung Cancer

(2012) K. D. Davies et al.   CLINICAL CANCER RESEARCH

Paracrine Receptor Activation by Microenvironment Triggers Bypass Survival Signals and ALK Inhibitor Resistance in EML4-ALK Lung Cancer Cells

(2012) T. Yamada et al.   CLINICAL CANCER RESEARCH

Activation of HER Family Signaling as a Mechanism of Acquired Resistance to ALK Inhibitors in EML4-ALK-Positive Non-Small Cell Lung Cancer

(2012) J. Tanizaki et al.   CLINICAL CANCER RESEARCH

The R1275Q Neuroblastoma Mutant and Certain ATP-competitive Inhibitors Stabilize Alternative Activation Loop Conformations of Anaplastic Lymphoma Kinase

(2012) Linda F. Epstein et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis

(2012) Weiwei Xue et al.   Journal of Chemical Information and Modeling

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

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

ROS1 Rearrangements Define a Unique Molecular Class of Lung Cancers

(2012) Kristin Bergethon et al.   JOURNAL OF CLINICAL ONCOLOGY

Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA

(2012) Matthieu Wilhelm et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular pathology of lung cancer: key to personalized medicine

(2012) Liang Cheng et al.   MODERN PATHOLOGY

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

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

(2012) J. Wereszczynski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study

(2012) Peter Michael Kekenes-Huskey et al.   PLoS Computational Biology

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

(2012) Yasuhiro Matsunaga et al.   PLoS Computational Biology

A Novel ALK Secondary Mutation and EGFR Signaling Cause Resistance to ALK Kinase Inhibitors

(2011) T. Sasaki et al.   CANCER RESEARCH

Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles

(2011) Yong Zhang et al.   Journal of Chemical Theory and Computation

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Structure Based Drug Design of Crizotinib (PF-02341066), a Potent and Selective Dual Inhibitor of Mesenchymal–Epithelial Transition Factor (c-MET) Kinase and Anaplastic Lymphoma Kinase (ALK)

(2011) J. Jean Cui et al.   JOURNAL OF MEDICINAL CHEMISTRY

Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix

(2011) Jen Hsin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Free Energy Calculations on the Two Drug Binding Sites in the M2 Proton Channel

(2011) Ruo-Xu Gu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Effect of Urea on the β-Hairpin Conformational Ensemble and Protein Denaturation Mechanism

(2011) Anna Berteotti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

One size does not fit all

(2011) Christine M. Lovly et al.   Nature Reviews Clinical Oncology

Personalized medicine in lung cancer: what we need to know

(2011) Tony S. K. Mok   Nature Reviews Clinical Oncology

The hidden energetics of ligand binding and activation in a glutamate receptor

(2011) Albert Y Lau et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

(2011) F. Marinelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Umbrella sampling

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

Drug–target residence time: critical information for lead optimization

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

Recognition of the Ring-Opened State of Proliferating Cell Nuclear Antigen by Replication Factor C Promotes Eukaryotic Clamp-Loading

(2010) John A. Tainer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Dynamics and Brownian Dynamics Investigation of Ion Permeation and Anesthetic Halothane Effects on a Proton-Gated Ion Channel

(2010) Mary Hongying Cheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Do Sterols Determine the Antifungal Activity of Amphotericin B? Free Energy of Binding between the Drug and Its Membrane Targets

(2010) Anna Neumann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

COT drives resistance to RAF inhibition through MAP kinase pathway reactivation

(2010) Cory M. Johannessen et al.   NATURE

Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation

(2010) Ramin Nazarian et al.   NATURE

EML4-ALK Mutations in Lung Cancer That Confer Resistance to ALK Inhibitors

(2010) Young Lim Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

A self-learning algorithm for biased molecular dynamics

(2010) Gareth A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance

(2010) J. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Permeation of Membranes by Ribose and Its Diastereomers

(2009) Chenyu Wei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Residence Time of Receptor−Ligand Complexes and Its Effect on Biological Function

(2008) Peter J. Tummino et al.   BIOCHEMISTRY

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes

(2008) Arnab Mukherjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

(2008) Massimiliano Bonomi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Binding of ADP in the Mitochondrial ADP/ATP Carrier Is Driven by an Electrostatic Funnel

(2008) François Dehez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Similar Membrane Affinity of Mono- and Di-S-acylated Ras Membrane Anchors: A New Twist in the Role of Protein Lipidation

(2008) Alemayehu A. Gorfe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

(2008) Anna Berteotti 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

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun 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