Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK

Anaplastic lymphoma kinase (ALK) inhibitors in the treatment of ALK-driven lung cancers

(2017) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation

(2017) Peichen Pan et al.   ACS Central Science

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

(2016) Quan Zou et al.   BMC Systems Biology

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1

(2016) Huiyong Sun 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

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

CHZ868, a Type II JAK2 Inhibitor, Reverses Type I JAK Inhibitor Persistence and Demonstrates Efficacy in Myeloproliferative Neoplasms

(2015) Sara C. Meyer et al.   CANCER CELL

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

FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors

(2015) C C Smith et al.   LEUKEMIA

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

Exploration of Type II Binding Mode: A Privileged Approach for Kinase Inhibitor Focused Drug Discovery?

(2014) Zheng Zhao et al.   ACS Chemical Biology

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification

(2014) Li Song et al.   BMC BIOINFORMATICS

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility

(2014) Sheng Tian et al.   Journal of Chemical Information and Modeling

First-Line Crizotinib versus Chemotherapy in ALK-Positive Lung Cancer

(2014) Benjamin J. Solomon et al.   NEW ENGLAND JOURNAL OF MEDICINE

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Huiyong Sun et al.   PLoS Computational Biology

Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs

(2013) Tomasz Frączek et al.   Journal of Chemical Information and Modeling

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures

(2013) Sheng Tian et al.   Journal of Chemical Information and Modeling

Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations

(2013) Yong-Liang Zhu et al.   Journal of Chemical Information and Modeling

Validated Conformational Ensembles Are Key for the Successful Prediction of Protein Complexes

(2013) Carles Pons 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

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crizotinib versus Chemotherapy in Advanced ALK-Positive Lung Cancer

(2013) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Potential and Limitations of Ensemble Docking

(2012) Oliver Korb et al.   Journal of Chemical Information and Modeling

GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations

(2012) David E. Tanner et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Rapid Development of Piperidine Carboxamides as Potent and Selective Anaplastic Lymphoma Kinase Inhibitors

(2012) Marian C. Bryan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Escaping ALK Inhibition: Mechanisms of and Strategies to Overcome Resistance

(2012) C. M. Lovly et al.   Science Translational Medicine

Mechanisms of Acquired Crizotinib Resistance in ALK-Rearranged Lung Cancers

(2012) R. Katayama et al.   Science Translational Medicine

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

(2011) Markus A. Lill   BIOCHEMISTRY

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

(2011) T. Sasaki et al.   CANCER RESEARCH

New Strategies for Treatment of ALK-Rearranged Non-Small Cell Lung Cancers

(2011) T. Sasaki et al.   CLINICAL CANCER RESEARCH

Influence of water–protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

(2011) Dietmar Paschek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Activation mechanism of the  2-adrenergic receptor

(2011) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

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

(2008) Peter J. Tummino et al.   BIOCHEMISTRY