| scholarly article | Q13442814 |
| P356 | DOI | 10.1111/CBDD.13148 |
| P698 | PubMed publication ID | 29139214 |
| P50 | author | Jianzhong Chen | Q69398575 |
| Xinguo Liu | Q89264019 | ||
| P2093 | author name string | Jing Su | |
| Qinggang Zhang | |||
| Shaolong Zhang | |||
| Fangfang Yan | |||
| P2860 | cites work | RVX-208, an inducer of ApoA-I in humans, is a BET bromodomain antagonist | Q21132391 |
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| 4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1) | Q27703416 | ||
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| Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains | Q27704993 | ||
| RVX-297- a novel BD2 selective inhibitor of BET bromodomains | Q27709485 | ||
| The Amber biomolecular simulation programs | Q27860745 | ||
| Targeting epigenetic readers in cancer | Q42714565 | ||
| Evaluating the potency of HIV-1 protease drugs to combat resistance | Q43196448 | ||
| Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. | Q43678172 | ||
| Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models | Q45179427 | ||
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| The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins | Q46719351 | ||
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| Effect of electrostatic polarization and bridging water on CDK2-ligand binding affinities calculated using a highly efficient interaction entropy method. | Q51075716 | ||
| Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy | Q51383023 | ||
| Clarifying binding difference of ATP and ADP to extracellular signal-regulated kinase 2 by using molecular dynamics simulations | Q51437778 | ||
| Fast and accurate computation schemes for evaluating vibrational entropy of proteins. | Q51605931 | ||
| Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations | Q52465150 | ||
| BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells | Q53328142 | ||
| 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 | Q54323649 | ||
| Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems | Q56750591 | ||
| Comparison of multiple Amber force fields and development of improved protein backbone parameters | Q27861040 | ||
| The bromodomain: a chromatin-targeting module? | Q28139513 | ||
| Targeting bromodomains: epigenetic readers of lysine acetylation | Q28238635 | ||
| Gene duplications in the structural evolution of chymotrypsin | Q28239251 | ||
| Inhibition of BET bromodomains as a therapeutic strategy for cancer drug discovery | Q28260105 | ||
| A novel, mitogen-activated nuclear kinase is related to a Drosophila developmental regulator | Q28275590 | ||
| Automated docking of flexible ligands: applications of AutoDock | Q28285420 | ||
| Binding modes of three inhibitors 8CA, F8A and I4A to A-FABP studied based on molecular dynamics simulation | Q28539602 | ||
| Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations | Q28818600 | ||
| Development and testing of a general amber force field | Q29547642 | ||
| Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation | Q29617869 | ||
| An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. | Q30168058 | ||
| Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. | Q30333153 | ||
| 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. | Q30835329 | ||
| PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data | Q31026348 | ||
| The structural basis of ATP as an allosteric modulator | Q34165655 | ||
| A novel BET bromodomain inhibitor, RVX-208, shows reduction of atherosclerosis in hyperlipidemic ApoE deficient mice. | Q34428881 | ||
| Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations | Q34531578 | ||
| Nonequivalent response to bromodomain-targeting BET inhibitors in oligodendrocyte cell fate decision | Q35208927 | ||
| Small molecule inhibitors of bromodomain-acetyl-lysine interactions | Q35535791 | ||
| Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin. | Q35812336 | ||
| Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation | Q36329555 | ||
| Accurate calculation of the absolute free energy of binding for drug molecules | Q36427764 | ||
| Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics | Q36494755 | ||
| Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy | Q37163377 | ||
| Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. | Q37334404 | ||
| Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis | Q37405719 | ||
| Affinity map of bromodomain protein 4 (BRD4) interactions with the histone H4 tail and the small molecule inhibitor JQ1. | Q37691709 | ||
| The bromodomain interaction module | Q38019699 | ||
| Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions | Q38038217 | ||
| Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations | Q38874308 | ||
| A theoretical study on the molecular determinants of the affibody protein Z(Aβ3) bound to an amyloid β peptide. | Q38997273 | ||
| Differential flap dynamics in l,d-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics. | Q40222330 | ||
| Ligand docking and binding site analysis with PyMOL and Autodock/Vina | Q40898209 | ||
| Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters | Q41245086 | ||
| Selective inhibition mechanism of RVX-208 to the second bromodomain of bromo and extraterminal proteins: insight from microsecond molecular dynamics simulations | Q41458992 | ||
| Numerical integration: a method for improving solution stability in models of the circulation | Q41917104 | ||
| 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 | Q41921801 | ||
| Dual-activity PI3K-BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis | Q42320410 | ||
| P4510 | describes a project that uses | molecular dynamics simulation | Q901663 |
| P433 | issue | 3 | |
| P304 | page(s) | 828-840 | |
| P577 | publication date | 2017-12-10 | |
| P1433 | published in | Chemical Biology and Drug Design | Q15749458 |
| P1476 | title | A theoretical insight into selectivity of inhibitors toward two domains of bromodomain-containing protein 4 using molecular dynamics simulations | |
| P478 | volume | 91 |
| Q99413660 | BRD4/8/9 are prognostic biomarkers and associated with immune infiltrates in hepatocellular carcinoma |
| Q90431599 | Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament |
| Q58710194 | Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5 |
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