Detalhe da pesquisa
1.
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking.
J Chem Inf Model;
64(10): 4158-4167, 2024 May 27.
Artigo
em Inglês
| MEDLINE
| ID: mdl-38751042
2.
Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability.
Proteins;
89(5): 502-511, 2021 05.
Artigo
em Inglês
| MEDLINE
| ID: mdl-33340163
3.
Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking.
J Chem Inf Model;
61(10): 5161-5171, 2021 10 25.
Artigo
em Inglês
| MEDLINE
| ID: mdl-34549581
4.
Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation.
J Chem Inf Model;
61(4): 1921-1930, 2021 04 26.
Artigo
em Inglês
| MEDLINE
| ID: mdl-33835817
5.
Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking.
J Comput Chem;
41(17): 1606-1615, 2020 06 30.
Artigo
em Inglês
| MEDLINE
| ID: mdl-32267975
6.
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns.
J Chem Inf Model;
60(6): 2803-2818, 2020 06 22.
Artigo
em Inglês
| MEDLINE
| ID: mdl-32469517
7.
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling.
J Chem Inf Model;
60(10): 4867-4880, 2020 10 26.
Artigo
em Inglês
| MEDLINE
| ID: mdl-32910853
8.
Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Biochemistry;
57(36): 5289-5300, 2018 09 11.
Artigo
em Inglês
| MEDLINE
| ID: mdl-30110540
9.
Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach.
J Comput Chem;
39(32): 2679-2689, 2018 12 15.
Artigo
em Inglês
| MEDLINE
| ID: mdl-30515903
10.
Structural and thermodynamic characterization of endo-1,3-ß-glucanase: Insights into the substrate recognition mechanism.
Biochim Biophys Acta Proteins Proteom;
1866(3): 415-425, 2018 Mar.
Artigo
em Inglês
| MEDLINE
| ID: mdl-29246508
11.
Model Building of Antibody-Antigen Complex Structures Using GBSA Scores.
J Chem Inf Model;
56(10): 2005-2012, 2016 10 24.
Artigo
em Inglês
| MEDLINE
| ID: mdl-27618247
12.
The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors.
J Chem Inf Model;
56(12): 2445-2456, 2016 12 27.
Artigo
em Inglês
| MEDLINE
| ID: mdl-28024406
13.
The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.
J Chem Phys;
140(19): 194307, 2014 May 21.
Artigo
em Inglês
| MEDLINE
| ID: mdl-24852538
14.
Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.
ACS Omega;
9(3): 3412-3422, 2024 Jan 23.
Artigo
em Inglês
| MEDLINE
| ID: mdl-38284074
15.
Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model.
J Chem Theory Comput;
20(1): 7-17, 2024 Jan 09.
Artigo
em Inglês
| MEDLINE
| ID: mdl-38148034
16.
Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations.
Methods Mol Biol;
2552: 151-163, 2023.
Artigo
em Inglês
| MEDLINE
| ID: mdl-36346591
17.
Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL.
Commun Biol;
6(1): 349, 2023 03 30.
Artigo
em Inglês
| MEDLINE
| ID: mdl-36997643
18.
Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.
Biophys Physicobiol;
20(4): e200047, 2023.
Artigo
em Inglês
| MEDLINE
| ID: mdl-38344029
19.
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.
Protein Sci;
32(10): e4775, 2023 Oct.
Artigo
em Inglês
| MEDLINE
| ID: mdl-37661929
20.
Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.
J Chem Phys;
137(5): 054314, 2012 Aug 07.
Artigo
em Inglês
| MEDLINE
| ID: mdl-22894355