Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

(2019) Jianzhong Chen et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

Inhibiting mechanism of small molecule toward the p53-MDM2 interaction: A molecular dynamic exploration

(2018) Jianzhong Chen et al.   Chemical Biology & Drug Design

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

(2018) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5

(2018) Fangfang Yan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Electrostatic Interaction-Mediated Conformational Changes of Adipocyte Fatty Acid Binding Protein Probed by Molecular Dynamics Simulation

(2018) Fangfang Yan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring Molecular Mechanism of Allosteric Inhibitor to Relieve Drug Resistance of Multiple Mutations in HIV-1 Protease by Enhanced Conformational Sampling

(2018) Jianzhong Chen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Characterizing the structural variability of HIV-2 protease upon the binding of diverse ligands using a structural alphabet approach

(2018) Dhoha Triki et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp et al.   Journal of Chemical Theory and Computation

Structural distortions due to missense mutations in human formylglycine-generating enzyme leading to multiple sulfatase deficiency

(2017) D. Meshach Paul et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis

(2017) Jianzhong Chen   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A computational insight into binding modes of inhibitors XD29, XD35, and XD28 to bromodomain-containing protein 4 based on molecular dynamics simulations

(2017) Jing Su et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Inhibition of β-Amyloid Channels with a Drug Candidate wgx-50 Revealed by Molecular Dynamics Simulations

(2017) Shuang Hou et al.   Journal of Chemical Information and Modeling

Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12

(2017) Xukai Jiang et al.   Journal of Chemical Information and Modeling

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

Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity

(2017) Danfeng Shi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Substrate-induced changes in dynamics and molecular motions of cuticle-degrading serine protease PL646: a molecular dynamics study

(2017) Li-Quan Yang et al.   RSC Advances

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

The environmental endocrine disruptor p-nitrophenol interacts with FKBP51, a positive regulator of androgen receptor and inhibits androgen receptor signaling in human cells

(2016) Dan Wu et al.   JOURNAL OF HAZARDOUS MATERIALS

Rapid, Structure-Based Exploration of Pipecolic Acid Amides as Novel Selective Antagonists of the FK506-Binding Protein 51

(2016) Steffen Gaali et al.   JOURNAL OF MEDICINAL CHEMISTRY

Redox-Responsive Fluorescent Probes with Different Design Strategies

(2015) Zhangrong Lou et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

Structure–Affinity Relationship Analysis of Selective FKBP51 Ligands

(2015) Xixi Feng et al.   JOURNAL OF MEDICINAL CHEMISTRY

Quantitative prediction of charge mobilities of π-stacked systems by first-principles simulation

(2015) Wei-Qiao Deng et al.   Nature Protocols

Rational Design and Asymmetric Synthesis of Potent and Neurotrophic Ligands for FK506-Binding Proteins (FKBPs)

(2014) Sebastian Pomplun et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Programming tools: Adventures with R

(2014) Sylvia Tippmann   NATURE

Selective inhibitors of the FK506-binding protein 51 by induced fit

(2014) Steffen Gaali et al.   Nature Chemical Biology

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

FKBPs and the Akt/mTOR pathway

(2013) Felix Hausch et al.   CELL CYCLE

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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Increasing the Efficiency of Ligands for FK506-Binding Protein 51 by Conformational Control

(2013) Yansong Wang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Large FK506-Binding Proteins Shape the Pharmacology of Rapamycin

(2013) A. M. Marz et al.   MOLECULAR AND CELLULAR BIOLOGY

The Prospect of FKBP51 as a Drug Target

(2012) Mathias V. Schmidt et al.   ChemMedChem

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

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

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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Evaluation of Synthetic FK506 Analogues as Ligands for the FK506-Binding Proteins 51 and 52

(2012) Ranganath Gopalakrishnan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Regulation of the glucocorticoid response to stress-related disorders by the Hsp90-binding immunophilin FKBP51

(2012) Natalia M. Galigniana et al.   JOURNAL OF NEUROCHEMISTRY

Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90

(2011) Andreas Bracher et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Chaperoning steroidal physiology: Lessons from mouse genetic models of Hsp90 and its cochaperones

(2011) Edwin R. Sanchez   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The Emerging Role of Large Immunophilin FK506 Binding Protein 51 in Cancer

(2011) S. Romano et al.   CURRENT MEDICINAL CHEMISTRY

FKBP51 and the NF-κB regulatory pathway in cancer

(2011) Simona Romano et al.   CURRENT OPINION IN PHARMACOLOGY

Organization and function of the FKBP52 and FKBP51 genes

(2011) Donna L Cioffi et al.   CURRENT OPINION IN PHARMACOLOGY

Targeting FKBP isoforms with small-molecule ligands

(2011) Elizabeth A Blackburn et al.   CURRENT OPINION IN PHARMACOLOGY

The 90-kDa Heat-shock Protein (Hsp90)-binding Immunophilin FKBP51 Is a Mitochondrial Protein That Translocates to the Nucleus to Protect Cells against Oxidative Stress

(2011) Luciana I. Gallo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

FKBP51 and FKBP52 in signaling and disease

(2011) Cheryl L. Storer et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Subcellular rearrangement of hsp90-binding immunophilins accompanies neuronal differentiation and neurite outgrowth

(2010) Héctor R. Quintá et al.   JOURNAL OF NEUROCHEMISTRY

The Hsp90 Cochaperone, FKBP51, Increases Tau Stability and Polymerizes Microtubules

(2010) U. K. Jinwal et al.   JOURNAL OF NEUROSCIENCE

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

Peptidyl-Prolyl Isomerase FKBP52 Controls Chemotropic Guidance of Neuronal Growth Cones via Regulation of TRPC1 Channel Opening

(2009) Sangwoo Shim et al.   NEURON

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

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

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

Molecular Dynamics Simulations of Hemoglobin A in Different States and Bound to DPG: Effector-Linked Perturbation of Tertiary Conformations and HbA Concerted Dynamics

(2007) Monique Laberge et al.   BIOPHYSICAL JOURNAL