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Biochemical simulations  
PLOS Computational Biology  
Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates

Alejandro Feito, Ignacio Sanchez-Burgos, Ignacio Tejero, Eduardo Sanz, Antonio Rey, Rosana Collepardo-Guevara, Andrés R. Tejedor, Jorge R. Espinosa

Research Article | published 13 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012737

Views: 657Citations: 0Saves: 0 • Shares: 0

Model supports asymmetric regulation across the intercellular junction for collective cell polarization

Katherine Levandosky, Calina Copos

Research Article | published 17 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012216

Views: 285Citations: 0Saves: 1 • Shares: 0

AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis

Michael Alexander Ramirez Sierra, Thomas R. Sokolowski

Research Article | published 14 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012473

Views: 694Citations: 0Saves: 0 • Shares: 0

Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1)

Rym Ben Boubaker, Daniel Henrion, Marie Chabbert

Research Article | published 13 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012559

Views: 435Citations: 0Saves: 1 • Shares: 1

A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors

Alireza Rezvani-Sharif, Hadi Lioe, Steven K. Dower, Matthias Pelzing, Con Panousis, Dalton J. E. Harvie, Ineke L. Muir

Research Article | published 04 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012552

Views: 783Citations: 1Saves: 0 • Shares: 0

IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation

Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang, Ruhong Zhou

Research Article | published 28 Oct 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012293

Views: 500Citations: 0Saves: 0 • Shares: 0

Alternate conformational trajectories in ribosome translocation

Jose L. Alejo, Dylan Girodat, Michael J. Hammerling, Jessica A. Willi, Michael C. Jewett, Aaron E. Engelhart, Katarzyna P. Adamala

Research Article | published 14 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012319

Views: 1160Citations: 0Saves: 4 • Shares: 7

Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force

Vasyl V. Mykuliak, Rolle Rahikainen, Neil J. Ball, Giovanni Bussi, Benjamin T. Goult, Vesa P. Hytönen

Research Article | published 07 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012341

Views: 1149Citations: 0Saves: 7 • Shares: 4

Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM

Jesper J. Madsen, Y. Zenmei Ohkubo

Research Article | published 08 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011421

Views: 928Citations: 1Saves: 0 • Shares: 0

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows

Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital, Modesto Orozco

Education | published 20 Jun 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012173

Views: 1069Citations: 0Saves: 7 • Shares: 0

Computational design of Periplasmic binding protein biosensors guided by molecular dynamics

Jack M. O’Shea, Peter Doerner, Annis Richardson, Christopher W. Wood

Research Article | published 17 Jun 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012212

Views: 1098Citations: 0Saves: 11 • Shares: 6

Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7

Akseli Niemelä, Artturi Koivuniemi

Research Article | published 28 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012137

Views: 633Citations: 0Saves: 0 • Shares: 0

Transferable deep generative modeling of intrinsically disordered protein conformations

Giacomo Janson, Michael Feig

Methods | published 23 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012144

Views: 1755Citations: 4Saves: 0 • Shares: 0

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface

Adam Husar, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey, Ali S. Saglam, James R. Faeder, Thomas M. Bartol, Mary B. Kennedy, Terrence J. Sejnowski

Software | published 24 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011800

Views: 1089Citations: 7Saves: 0 • Shares: 0

Computational prediction of protein interactions in single cells by proximity sequencing

Junjie Xia, Hoang Van Phan, Luke Vistain, Mengjie Chen, Aly A. Khan, Savaş Tay

Research Article | published 14 Mar 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011915

Views: 1306Citations: 1Saves: 2 • Shares: 2

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