Detalhe da pesquisa
1.
Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity.
Bioorg Med Chem
; 103: 117577, 2024 Apr 01.
Artigo
em Inglês
| MEDLINE | ID: mdl-38518735
2.
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
J Am Chem Soc
; 137(7): 2695-703, 2015 Feb 25.
Artigo
em Inglês
| MEDLINE | ID: mdl-25625324
3.
Deconstructing activation events in rhodopsin.
J Am Chem Soc
; 135(30): 10906-9, 2013 Jul 31.
Artigo
em Inglês
| MEDLINE | ID: mdl-23841875
4.
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.
J Comput Chem
; 34(11): 893-903, 2013 Apr 30.
Artigo
em Inglês
| MEDLINE | ID: mdl-23292859
5.
MATCH: an atom-typing toolset for molecular mechanics force fields.
J Comput Chem
; 33(2): 189-202, 2012 Jan 15.
Artigo
em Inglês
| MEDLINE | ID: mdl-22042689
6.
Surveying implicit solvent models for estimating small molecule absolute hydration free energies.
J Comput Chem
; 32(13): 2909-23, 2011 Oct.
Artigo
em Inglês
| MEDLINE | ID: mdl-21735452
7.
Applying efficient implicit nongeometric constraints in alchemical free energy simulations.
J Comput Chem
; 32(16): 3423-32, 2011 Dec.
Artigo
em Inglês
| MEDLINE | ID: mdl-21919014
8.
On the mechanism of crystalline polymorph selection by polymer heteronuclei.
Langmuir
; 27(12): 7575-9, 2011 Jun 21.
Artigo
em Inglês
| MEDLINE | ID: mdl-21591791
9.
Lambda-dynamics free energy simulation methods.
J Comput Chem
; 30(11): 1692-700, 2009 Aug.
Artigo
em Inglês
| MEDLINE | ID: mdl-19421993
10.
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
J Chem Theory Comput
; 12(1): 281-96, 2016 Jan 12.
Artigo
em Inglês
| MEDLINE | ID: mdl-26584231
11.
Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods.
J Chem Theory Comput
; 10(8): 3207-20, 2014 Aug 12.
Artigo
em Inglês
| MEDLINE | ID: mdl-26588291
12.
pH-dependent dynamics of complex RNA macromolecules.
J Chem Theory Comput
; 9(2): 935-943, 2013 Feb 12.
Artigo
em Inglês
| MEDLINE | ID: mdl-23525495
13.
Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.
J Phys Chem Lett
; 4(5): 760-766, 2013 Mar 07.
Artigo
em Inglês
| MEDLINE | ID: mdl-23526474
14.
Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.
J Chem Theory Comput
; 9(2): 1282-93, 2013 Feb 12.
Artigo
em Inglês
| MEDLINE | ID: mdl-26588769
15.
Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.
J Chem Theory Comput
; 8(1): 36-46, 2012 Jan 10.
Artigo
em Inglês
| MEDLINE | ID: mdl-22337595
16.
Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies.
J Chem Theory Comput
; 7(9): 2728-2739, 2011 Sep 13.
Artigo
em Inglês
| MEDLINE | ID: mdl-22125476
17.
Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design.
J Chem Theory Comput
; 5(6): 1680-1691, 2009.
Artigo
em Inglês
| MEDLINE | ID: mdl-20046995
18.
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.
Acta Crystallogr D Biol Crystallogr
; 64(Pt 4): 383-96, 2008 Apr.
Artigo
em Inglês
| MEDLINE | ID: mdl-18391405
19.
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.
ACS Chem Biol
; 1(11): 702-12, 2006 Dec 20.
Artigo
em Inglês
| MEDLINE | ID: mdl-17184135
20.
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.
Biophys J
; 88(2): 925-38, 2005 Feb.
Artigo
em Inglês
| MEDLINE | ID: mdl-15542547