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1.
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations.
Proc Natl Acad Sci U S A
; 120(12): e2221048120, 2023 03 21.
Artículo
en Inglés
| MEDLINE | ID: mdl-36920924
2.
Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes.
Proc Natl Acad Sci U S A
; 119(12): e2116543119, 2022 03 22.
Artículo
en Inglés
| MEDLINE | ID: mdl-35298336
3.
Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.
J Chem Phys
; 160(12)2024 Mar 28.
Artículo
en Inglés
| MEDLINE | ID: mdl-38516972
4.
Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.
Proc Natl Acad Sci U S A
; 118(17)2021 04 27.
Artículo
en Inglés
| MEDLINE | ID: mdl-33883282
5.
Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently.
J Am Chem Soc
; 145(18): 9916-9927, 2023 05 10.
Artículo
en Inglés
| MEDLINE | ID: mdl-37104720
6.
EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules.
J Comput Chem
; 44(17): 1536-1549, 2023 06 30.
Artículo
en Inglés
| MEDLINE | ID: mdl-36856731
7.
Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.
J Chem Phys
; 159(13)2023 Oct 07.
Artículo
en Inglés
| MEDLINE | ID: mdl-37787134
8.
RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics.
Phys Chem Chem Phys
; 24(3): 1462-1474, 2022 Jan 19.
Artículo
en Inglés
| MEDLINE | ID: mdl-34985469
9.
On the advantages of exploiting memory in Markov state models for biomolecular dynamics.
J Chem Phys
; 153(1): 014105, 2020 Jul 07.
Artículo
en Inglés
| MEDLINE | ID: mdl-32640825
10.
TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules.
J Chem Phys
; 150(12): 124105, 2019 Mar 28.
Artículo
en Inglés
| MEDLINE | ID: mdl-30927873
11.
Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.
J Chem Phys
; 143(5): 054110, 2015 Aug 07.
Artículo
en Inglés
| MEDLINE | ID: mdl-26254645
12.
Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate.
J Phys Chem B
; 128(10): 2347-2359, 2024 Mar 14.
Artículo
en Inglés
| MEDLINE | ID: mdl-38416758
13.
The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules.
J Phys Chem B
; 126(43): 8632-8645, 2022 11 03.
Artículo
en Inglés
| MEDLINE | ID: mdl-36282904
14.
Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning.
JACS Au
; 1(9): 1330-1341, 2021 Sep 27.
Artículo
en Inglés
| MEDLINE | ID: mdl-34604842
15.
Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex.
Commun Biol
; 4(1): 1345, 2021 11 30.
Artículo
en Inglés
| MEDLINE | ID: mdl-34848812
16.
Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain.
RSC Chem Biol
; 2(4): 1274-1284, 2021 Aug 05.
Artículo
en Inglés
| MEDLINE | ID: mdl-34458841
17.
Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect.
Nat Commun
; 8: 15639, 2017 05 31.
Artículo
en Inglés
| MEDLINE | ID: mdl-28561067
18.
Interactions of a water-soluble fullerene derivative with amyloid-ß protofibrils: dynamics, binding mechanism, and the resulting salt-bridge disruption.
J Phys Chem B
; 118(24): 6733-41, 2014 Jun 19.
Artículo
en Inglés
| MEDLINE | ID: mdl-24857343
19.
Transformation of an oblate-shaped vesicle induced by an adhering spherical particle.
Phys Rev E Stat Nonlin Soft Matter Phys
; 84(5 Pt 1): 050901, 2011 Nov.
Artículo
en Inglés
| MEDLINE | ID: mdl-22181362
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