Detalhe da pesquisa
1.
MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization.
Nucleic Acids Res
; 2024 May 23.
Artigo
em Inglês
| MEDLINE | ID: mdl-38783081
2.
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.
J Chem Inf Model
; 63(3): 973-985, 2023 02 13.
Artigo
em Inglês
| MEDLINE | ID: mdl-36638318
3.
Sampling constrained stochastic trajectories using Brownian bridges.
J Chem Phys
; 157(5): 054105, 2022 Aug 07.
Artigo
em Inglês
| MEDLINE | ID: mdl-35933198
4.
Parameterizing elastic network models to capture the dynamics of proteins.
J Comput Chem
; 42(23): 1643-1661, 2021 09 05.
Artigo
em Inglês
| MEDLINE | ID: mdl-34117647
5.
Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.
Proc Natl Acad Sci U S A
; 115(52): E12172-E12181, 2018 12 26.
Artigo
em Inglês
| MEDLINE | ID: mdl-30541892
6.
Statistical Physics Approach to the Optimal Transport Problem.
Phys Rev Lett
; 123(4): 040603, 2019 Jul 26.
Artigo
em Inglês
| MEDLINE | ID: mdl-31491256
7.
Eleven quick tips for running an interdisciplinary short course for new graduate students.
PLoS Comput Biol
; 14(3): e1006039, 2018 03.
Artigo
em Inglês
| MEDLINE | ID: mdl-29596417
8.
Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State.
J Biol Chem
; 292(5): 1550-1558, 2017 02 03.
Artigo
em Inglês
| MEDLINE | ID: mdl-27986812
9.
Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments.
Molecules
; 24(1)2018 Dec 28.
Artigo
em Inglês
| MEDLINE | ID: mdl-30597916
10.
String kernels for protein sequence comparisons: improved fold recognition.
BMC Bioinformatics
; 18(1): 137, 2017 Feb 28.
Artigo
em Inglês
| MEDLINE | ID: mdl-28245816
11.
A weighted string kernel for protein fold recognition.
BMC Bioinformatics
; 18(1): 378, 2017 Aug 25.
Artigo
em Inglês
| MEDLINE | ID: mdl-28841820
12.
Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.
EMBO J
; 32(5): 728-41, 2013 Mar 06.
Artigo
em Inglês
| MEDLINE | ID: mdl-23403925
13.
Ab initio sampling of transition paths by conditioned Langevin dynamics.
J Chem Phys
; 147(15): 152703, 2017 Oct 21.
Artigo
em Inglês
| MEDLINE | ID: mdl-29055326
14.
Minimum action transition paths connecting minima on an energy surface.
J Chem Phys
; 145(18): 184111, 2016 Nov 14.
Artigo
em Inglês
| MEDLINE | ID: mdl-27846680
15.
Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif.
J Biol Chem
; 289(7): 4367-76, 2014 Feb 14.
Artigo
em Inglês
| MEDLINE | ID: mdl-24394410
16.
Protein side-chain modeling with a protein-dependent optimized rotamer library.
Proteins
; 82(9): 2000-17, 2014 Sep.
Artigo
em Inglês
| MEDLINE | ID: mdl-24623614
17.
Identifying essential pairwise interactions in elastic network model using the alpha shape theory.
J Comput Chem
; 35(15): 1111-21, 2014 Jun 05.
Artigo
em Inglês
| MEDLINE | ID: mdl-24648309
18.
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.
Biophys J
; 104(3): 683-93, 2013 Feb 05.
Artigo
em Inglês
| MEDLINE | ID: mdl-23442919
19.
Extracting knowledge from protein structure geometry.
Proteins
; 81(5): 841-51, 2013 May.
Artigo
em Inglês
| MEDLINE | ID: mdl-23280479
20.
Capturing protein sequence-structure specificity using computational sequence design.
Proteins
; 81(9): 1556-70, 2013 Sep.
Artigo
em Inglês
| MEDLINE | ID: mdl-23609941