Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2

Hepatoma cell functions modulated by NEK2 are associated with liver cancer progression

(2017) Sheng-Ming Wu et al.   INTERNATIONAL JOURNAL OF CANCER

Nek2 siRNA therapy using a portal venous port-catheter system for liver metastasis in pancreatic cancer

(2016) Toshio Kokuryo et al.   CANCER SCIENCE

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

Increased NEK2 in hepatocellular carcinoma promotes cancer progression and drug resistance by promoting PP1/Akt and Wnt activation

(2016) Sailan Wen et al.   ONCOLOGY REPORTS

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease

(2015) Nan Li et al.   Journal of Chemical Information and Modeling

Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches

(2015) Lei Xu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Insights into the effects of mutations on Cren7–DNA binding using molecular dynamics simulations and free energy calculations

(2015) Lin Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors

(2015) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Overexpression of NIMA-related kinase 2 is associated with progression and poor prognosis of prostate cancer

(2015) Yan-Ru Zeng et al.   BMC Urology

Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation

(2014) Qifeng Bai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Exploring the mechanism how Marburg virus VP35 recognizes and binds dsRNA by molecular dynamics simulations and free energy calculations

(2014) Qiao Xue et al.   BIOPOLYMERS

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

Discovery of 4-Aryl-N-arylcarbonyl-2-aminothiazoles as Hec1/Nek2 Inhibitors. Part I: Optimization of in Vitro Potencies and Pharmacokinetic Properties

(2014) Ying-Shuan E. Lee et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Inhibitors Targeting the Macrophage Migration Inhibitory Factor via Structure-Based Virtual Screening and Bioassays

(2014) Lei Xu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Overexpression of the Nek2 kinase in colorectal cancer correlates with beta-catenin relocalization and shortened cancer-specific survival

(2014) Christopher P. Neal et al.   JOURNAL OF SURGICAL ONCOLOGY

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

Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation

(2014) Qifeng Bai 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

Up-regulation of NEK2 by MicroRNA-128 Methylation is Associated with Poor Prognosis in Colorectal Cancer

(2013) Yusuke Takahashi et al.   ANNALS OF SURGICAL ONCOLOGY

Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations

(2013) Peichen Pan et al.   ANTIVIRAL RESEARCH

NEK2 Induces Drug Resistance Mainly through Activation of Efflux Drug Pumps and Is Associated with Poor Prognosis in Myeloma and Other Cancers

(2013) Wen Zhou et al.   CANCER CELL

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

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

Modeling Compound–Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design

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

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

Role of Nek2 on centrosome duplication and aneuploidy in breast cancer cells

(2013) P Cappello et al.   ONCOGENE

Cdk4 and Nek2 Signal Binucleation and Centrosome Amplification in a Her2+ Breast Cancer Model

(2013) Mary Kathryn Harrison Pitner et al.   PLoS One

Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study

(2012) Dabo Pan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Cell cycle regulation by the NEK family of protein kinases

(2012) A. M. Fry et al.   JOURNAL OF CELL SCIENCE

Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase

(2012) Lin Li et al.   Journal of Chemical Information and Modeling

Design of Potent and Selective Hybrid Inhibitors of the Mitotic Kinase Nek2: Structure–Activity Relationship, Structural Biology, and Cellular Activity

(2012) Paolo Innocenti et al.   JOURNAL OF MEDICINAL CHEMISTRY

Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

(2012) Tingjun Hou et al.   JOURNAL OF PROTEOME RESEARCH

Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations

(2012) Mingyun Shen et al.   Molecular BioSystems

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy

(2011) Tingjun Hou et al.   BIOINFORMATICS

Plk1 Controls the Nek2A-PP1γ Antagonism in Centrosome Disjunction

(2011) Balca R. Mardin et al.   CURRENT BIOLOGY

Abnormal expression of Nek2 and β-catenin in breast carcinoma: clinicopathological correlations

(2011) Shuling Wang et al.   HISTOPATHOLOGY

Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship

(2011) Savade Solanki et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Nek family of kinases in cell cycle, checkpoint control and cancer

(2011) Larissa Moniz et al.   Cell Division

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

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

(2010) Jeremy R. Greenwood et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: SAR and Structural Characterization

(2010) Daniel K. Whelligan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Components of the Hippo pathway cooperate with Nek2 kinase to regulate centrosome disjunction

(2010) Balca R. Mardin et al.   NATURE CELL BIOLOGY

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

Synthesis and Biological Evaluation of a Series of Novel Inhibitor of Nek2/Hec1 Analogues

(2009) Xiao-Long Qiu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small Molecule Targeting the Hec1/Nek2 Mitotic Pathway Suppresses Tumor Cell Growth in Culture and in Animal

(2008) G. Wu et al.   CANCER RESEARCH

Nek2 as a novel molecular target for the treatment of breast carcinoma

(2008) Nobuyuki Tsunoda et al.   CANCER SCIENCE

Increased expression and nuclear localization of the centrosomal kinase Nek2 in human testicular seminomas

(2008) Federica Barbagallo et al.   JOURNAL OF PATHOLOGY

Predicting drug resistance of the HIV-1 protease using molecular interaction energy components

(2008) Tingjun Hou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

-Catenin is a Nek2 substrate involved in centrosome separation

(2007) S. Bahmanyar et al.   GENES & DEVELOPMENT

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY