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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.
Artículo
en Inglés
| 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.
Artículo
en Inglés
| 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.
Artículo
en Inglés
| MEDLINE | ID: mdl-34549581
4.
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.
Artículo
en Inglés
| MEDLINE | ID: mdl-32267975
5.
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Nucleic Acids Res
; 45(D1): D282-D288, 2017 01 04.
Artículo
en Inglés
| MEDLINE | ID: mdl-27789697
6.
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.
Artículo
en Inglés
| MEDLINE | ID: mdl-30110540
7.
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.
Artículo
en Inglés
| MEDLINE | ID: mdl-29246508
8.
Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.
ACS Omega
; 9(3): 3412-3422, 2024 Jan 23.
Artículo
en Inglés
| MEDLINE | ID: mdl-38284074
9.
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.
Artículo
en Inglés
| MEDLINE | ID: mdl-38148034
10.
Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations.
Methods Mol Biol
; 2552: 151-163, 2023.
Artículo
en Inglés
| MEDLINE | ID: mdl-36346591
11.
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.
Artículo
en Inglés
| MEDLINE | ID: mdl-36997643
12.
Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.
Biophys Physicobiol
; 20(4): e200047, 2023.
Artículo
en Inglés
| MEDLINE | ID: mdl-38344029
13.
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.
Artículo
en Inglés
| MEDLINE | ID: mdl-37661929
14.
Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking.
Biophys Rev
; 14(6): 1349-1358, 2022 Dec.
Artículo
en Inglés
| MEDLINE | ID: mdl-36659995
15.
History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics.
Biophys Rev
; 14(6): 1233-1238, 2022 Dec.
Artículo
en Inglés
| MEDLINE | ID: mdl-36532871
16.
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.
Protein Sci
; 31(1): 173-186, 2022 01.
Artículo
en Inglés
| MEDLINE | ID: mdl-34664328
17.
Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.
Sci Rep
; 12(1): 13792, 2022 08 13.
Artículo
en Inglés
| MEDLINE | ID: mdl-35963875
18.
Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.
Methods Mol Biol
; 2266: 187-202, 2021.
Artículo
en Inglés
| MEDLINE | ID: mdl-33759128
19.
N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations.
J Phys Chem B
; 125(49): 13376-13384, 2021 12 16.
Artículo
en Inglés
| MEDLINE | ID: mdl-34856806
20.
Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization.
Methods Enzymol
; 648: 159-185, 2021.
Artículo
en Inglés
| MEDLINE | ID: mdl-33579402