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1.
Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility.
J Chem Inf Model
; 63(6): 1695-1707, 2023 03 27.
Article
in English
| MEDLINE | ID: mdl-36916514
2.
Accurate Sampling of Macromolecular Conformations Using Adaptive Deep Learning and Coarse-Grained Representation.
J Chem Inf Model
; 62(7): 1602-1617, 2022 04 11.
Article
in English
| MEDLINE | ID: mdl-35352898
3.
Conformational Changes of Thyroid Receptors in Response to Antagonists.
J Chem Inf Model
; 61(2): 1010-1019, 2021 02 22.
Article
in English
| MEDLINE | ID: mdl-33449688
4.
Computational Assessment of Combination Therapy of Androgen Receptor-Targeting Compounds.
J Chem Inf Model
; 61(2): 1001-1009, 2021 02 22.
Article
in English
| MEDLINE | ID: mdl-33523669
5.
Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2.
Int J Mol Sci
; 22(4)2021 Feb 19.
Article
in English
| MEDLINE | ID: mdl-33669738
6.
Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds.
Int J Mol Sci
; 21(10)2020 May 21.
Article
in English
| MEDLINE | ID: mdl-32455534
7.
Modeling of Halogen-Protein Interactions in Co-Solvent Molecular Dynamics Simulations.
J Chem Inf Model
; 59(1): 38-42, 2019 01 28.
Article
in English
| MEDLINE | ID: mdl-30525593
8.
Molecular Determinants of the Differential Modulation of Cav1.2 and Cav1.3 by Nifedipine and FPL 64176.
Mol Pharmacol
; 94(3): 973-983, 2018 09.
Article
in English
| MEDLINE | ID: mdl-29980657
9.
Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites.
J Chem Inf Model
; 58(11): 2183-2188, 2018 11 26.
Article
in English
| MEDLINE | ID: mdl-30289252
10.
Molecular Modeling Evaluation of the Enantiomers of a Novel Adenylyl Cyclase 2 Inhibitor.
J Chem Inf Model
; 57(2): 322-334, 2017 02 27.
Article
in English
| MEDLINE | ID: mdl-28068084
11.
Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations.
J Comput Chem
; 37(20): 1861-5, 2016 07.
Article
in English
| MEDLINE | ID: mdl-27232548
12.
Structural transitions and interactions in the early stages of human glucagon amyloid fibrillation.
Biophys J
; 108(4): 937-948, 2015 Feb 17.
Article
in English
| MEDLINE | ID: mdl-25692598
13.
Substrate tunnels in enzymes: structure-function relationships and computational methodology.
Proteins
; 83(4): 599-611, 2015 Apr.
Article
in English
| MEDLINE | ID: mdl-25663659
14.
Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates.
Pharm Res
; 32(3): 986-1001, 2015 Mar.
Article
in English
| MEDLINE | ID: mdl-25208877
15.
Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.
Proteins
; 82(12): 3450-65, 2014 Dec.
Article
in English
| MEDLINE | ID: mdl-25269778
16.
WATsite: hydration site prediction program with PyMOL interface.
J Comput Chem
; 35(16): 1255-60, 2014 Jun 15.
Article
in English
| MEDLINE | ID: mdl-24752524
17.
Including ligand-induced protein flexibility into protein tunnel prediction.
J Comput Chem
; 35(24): 1748-56, 2014 Sep 15.
Article
in English
| MEDLINE | ID: mdl-25043499
18.
Analysis of factors influencing hydration site prediction based on molecular dynamics simulations.
J Chem Inf Model
; 54(10): 2987-95, 2014 Oct 27.
Article
in English
| MEDLINE | ID: mdl-25252619
19.
Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity.
Biochemistry
; 52(20): 3564-78, 2013 May 21.
Article
in English
| MEDLINE | ID: mdl-23617878
20.
Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking.
J Chem Inf Model
; 53(5): 1179-90, 2013 May 24.
Article
in English
| MEDLINE | ID: mdl-23621564