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Molecular dynamics

Fast exploration of an optimal path on the multidimensional free energy surface

Changjun Chen

Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors

Ornella Di Pietro, Jordi Juárez-Jiménez, [ ... ], F. Javier Luque

SAS profile correlations reveal SAS hierarchical nature and information content

Yannick G. Spill, Michael Nilges

Water permeation through the internal water pathway in activated GPCR rhodopsin

Katsufumi Tomobe, Eiji Yamamoto, Kholmirzo Kholmurodov, Kenji Yasuoka

A prion-like mechanism for the propagated misfolding of SOD1 from in silico modeling of solvated near-native conformers

Eamonn F. Healy

EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay

Tobias Kroeger, Benedikt Frieg, [ ... ], Holger Gohlke

Computational study of aggregation mechanism in human lysozyme[D67H]

Dharmeshkumar Patel, Serdar Kuyucak

Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm⁵U present at ‘wobble’ position in anticodon loop of tRNA^Leu: A molecular modeling approach

Asmita S. Kamble, Prayagraj M. Fandilolu, Susmit B. Sambhare, Kailas D. Sonawane

The influence of cell membrane and SNAP25 linker loop on the dynamics and unzipping of SNARE complex

Yi Shi, Yong Zhang, Jizhong Lou

In silico design of the first DNA-independent mechanism-based inhibitor of mammalian DNA methyltransferase Dnmt1

Vedran Miletić, Ivica Odorčić, Patrik Nikolić, Željko M. Svedružić

Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations

Rainer Bomblies, Manuel Patrick Luitz, [ ... ], Martin Zacharias

Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer

Kota Kasahara, Masaaki Shiina, [ ... ], Haruki Nakamura

Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential

Katja Ostermeir, Martin Zacharias

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