Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling

Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations

(2017) Guodong Hu et al.   Journal of Chemical Information and Modeling

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Energetics and structural characterization of the “DFG-flip” conformational transition of B-RAF kinase: a SITS molecular dynamics study

(2017) Qiang Shao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling

(2017) Jianzhong Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effect of electrostatic polarization and bridging water on CDK2–ligand binding affinities calculated using a highly efficient interaction entropy method

(2017) Lili Duan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Design and synthesis of novel selective anaplastic lymphoma kinase inhibitors

(2016) Pierre-Yves Michellys et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Clarifying binding difference of ATP and ADP to extracellular signal-regulated kinase 2 by using molecular dynamics simulations

(2016) Jianzhong Chen   Chemical Biology & Drug Design

Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer’s Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies

(2016) Son Tung Ngo et al.   Journal of Chemical Information and Modeling

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

(2016) Xiangyu Jia et al.   Journal of Chemical Theory and Computation

Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay–Berne and Electric Multipole Potentials

(2016) Guohui Li et al.   Journal of Chemical Theory and Computation

Pyrazolylamine Derivatives Reveal the Conformational Switching between Type I and Type II Binding Modes of Anaplastic Lymphoma Kinase (ALK)

(2016) Chih-Hsiang Tu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy

(2016) Lili Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Resensitization to Crizotinib by the Lorlatinib ALK Resistance Mutation L1198F

(2016) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis

(2016) Jianzhong Chen et al.   Scientific Reports

Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

(2016) Li L. Duan et al.   Scientific Reports

Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations

(2015) Guodong Hu et al.   Chemical Biology & Drug Design

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

(2015) Jianzhong Chen et al.   Journal of Chemical Information and Modeling

Novel covalent modification of human anaplastic lymphoma kinase (ALK) and potentiation of crizotinib-mediated inhibition of ALK activity by BNP7787

(2015) Aulma Parker et al.   OncoTargets and Therapy

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

Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir

(2015) Yuqi Yu et al.   Scientific Reports

Managing treatment–related adverse events associated with Alk inhibitors

(2014) J.M. Rothenstein et al.   Current Oncology

Design of Potent and Selective Inhibitors to Overcome Clinical Anaplastic Lymphoma Kinase Mutations Resistant to Crizotinib

(2014) Qinhua Huang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of (10R)-7-Amino-12-fluoro-2,10,16-trimethyl-15-oxo-10,15,16,17-tetrahydro-2H-8,4-(metheno)pyrazolo[4,3-h][2,5,11]-benzoxadiazacyclotetradecine-3-carbonitrile (PF-06463922), a Macrocyclic Inhibitor of Anaplastic Lymphoma Kinase (ALK) and c-ros Oncogene 1 (ROS1) with Preclinical Brain Exposure and Broad-Spectrum Potency against ALK-Resistant Mutations

(2014) Ted W. Johnson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Mapping Central α-Helix Linker Mediated Conformational Transition Pathway of Calmodulin via Simple Computational Approach

(2014) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Selective Anaplastic Lymphoma Receptor Tyrosine Kinase Inhibitor ASP3026 Induces Tumor Regression and Prolongs Survival in Non-Small Cell Lung Cancer Model Mice

(2014) M. Mori et al.   MOLECULAR CANCER THERAPEUTICS

The Structural Basis of ATP as an Allosteric Modulator

(2014) Shaoyong Lu et al.   PLoS Computational Biology

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

(2013) Sander Pronk et al.   BIOINFORMATICS

PLUMED 2: New feathers for an old bird

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

A Comparative Molecular Dynamics, MM–PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV-1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants

(2013) Haralambos Tzoupis et al.   Journal of Chemical Theory and Computation

A New Quantum Calibrated Force Field for Zinc–Protein Complex

(2013) Tong Zhu et al.   Journal of Chemical Theory and Computation

ALKin Lung Cancer: Past, Present, and Future

(2013) Alice T. Shaw et al.   JOURNAL OF CLINICAL ONCOLOGY

Synthesis, Structure–Activity Relationships, and in Vivo Efficacy of the Novel Potent and Selective Anaplastic Lymphoma Kinase (ALK) Inhibitor 5-Chloro-N2-(2-isopropoxy-5-methyl-4-(piperidin-4-yl)phenyl)-N4-(2-(isopropylsulfonyl)phenyl)pyrimidine-2,4-diamine (LDK378) Currently in Phase 1 and Phase 2 Clinical Trials

(2013) Thomas H. Marsilje et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring Transition Pathway and Free-Energy Profile of Large-Scale Protein Conformational Change by Combining Normal Mode Analysis and Umbrella Sampling Molecular Dynamics

(2013) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Identification of Anaplastic Lymphoma Kinase as a Potential Therapeutic Target in Ovarian Cancer

(2012) H. Ren et al.   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

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

(2012) Vytautas Gapsys et al.   Journal of Chemical Theory and Computation

Activity and safety of crizotinib in patients with ALK-positive non-small-cell lung cancer: updated results from a phase 1 study

(2012) D Ross Camidge et al.   LANCET ONCOLOGY

Anaplastic lymphoma kinase (ALK): Structure, oncogenic activation, and pharmacological inhibition

(2012) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Anaplastic Thyroid Cancers Harbor Novel Oncogenic Mutations of the ALK Gene

(2011) A. K. Murugan et al.   CANCER RESEARCH

Targeting Anaplastic Lymphoma Kinase in Lung Cancer

(2011) A. T. Shaw et al.   CLINICAL CANCER RESEARCH

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

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

Anaplastic Lymphoma Kinase Translocation: A Predictive Biomarker of Pemetrexed in Patients with Non-small Cell Lung Cancer

(2011) Jeong-Ok Lee et al.   Journal of Thoracic Oncology

Crystal structure of the ALK (anaplastic lymphoma kinase) catalytic domain

(2010) Christian C. Lee et al.   BIOCHEMICAL JOURNAL

Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding

(2010) Ming-Jun Yang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Molecular dynamics simulation of SRP GTPases: Towards an understanding of the complex formation from equilibrium fluctuations

(2010) Mingjun Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Anaplastic lymphoma kinase: role in cancer pathogenesis and small-molecule inhibitor development for therapy

(2009) Thomas R Webb et al.   Expert Review of Anticancer Therapy

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Genomic Alterations of Anaplastic Lymphoma Kinase May Sensitize Tumors to Anaplastic Lymphoma Kinase Inhibitors

(2008) U. McDermott et al.   CANCER RESEARCH

Non-solid oncogenes in solid tumors:EML4-ALKfusion genes in lung cancer

(2008) Hiroyuki Mano   CANCER SCIENCE

Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study

(2008) Emilia L. Wu et al.   CHEMISTRY-A EUROPEAN JOURNAL

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of ALK as a major familial neuroblastoma predisposition gene

(2008) Yaël P. Mossé et al.   NATURE

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS