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PLOS Computational Biology  
Specificity and tunability of efflux pumps: A new role for the proton gradient?

Matthew Gerry, Duncan Kirby, Boian S Alexandrov, Dvira Segal, Anton Zilman

Research Article | published 27 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012772

Views: 60Citations: 0Saves: 0 • Shares: 0

A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation

Nan Wu, Zhi-Chao Xu, Kai-Dong Du, Shen Huang, Naohiro Kobayashi, Yutaka Kuroda, Yan-Hong Bai

Research Article | published 21 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012722

Views: 227Citations: 0Saves: 0 • Shares: 0

Predicting lung aging using scRNA-Seq data

Qi Song, Alex Singh, John E. McDonough, Taylor S. Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J. Ceulemans, Bart M. Vanaudenaerde, Wim A. Wuyts, Xiting Yan, Jonas Schupp, James S. Hagood, Naftali Kaminski, Ziv Bar-Joseph

Research Article | published 19 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012632

Views: 1046Citations: 0Saves: 1 • Shares: 19

A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission

Anna K. Leinheiser, Colleen C. Mitchell, Ethan Rooke, Stefan Strack, Chad E. Grueter

Research Article | published 18 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012596

Views: 440Citations: 0Saves: 0 • Shares: 0

PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites

Yun Zuo, Xingze Fang, Jiayong Wan, Wenying He, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng

Research Article | published 22 Oct 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012544

Views: 542Citations: 0Saves: 0 • Shares: 0

A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function

Andrew A. Schmidt, Alexander Y. Grosberg, Anna Grosberg

Research Article | published 05 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012321

Views: 941Citations: 0Saves: 0 • Shares: 0

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Vinoth Manivannan, Mandar M. Inamdar, Ranjith Padinhateeri

Research Article | published 11 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012235

Views: 532Citations: 0Saves: 0 • Shares: 0

Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors

Christina M. P. Ray, Huilin Yang, Jamie B. Spangler, Feilim Mac Gabhann

Research Article | published 07 Jun 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012157

Views: 1043Citations: 1Saves: 0 • Shares: 0

A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis

Florian E. C. Blanc, Anne Houdusse, Marco Cecchini

Research Article | published 25 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012005

Views: 735Citations: 1Saves: 6 • Shares: 3

Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations

Jong Hyuk Byun, Hye Seon Jeon, Hwi-yeol Yun, Jae Kyoung Kim

Research Article | published 24 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012066

Views: 1480Citations: 2Saves: 3 • Shares: 2

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: 1090Citations: 7Saves: 0 • Shares: 0

Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly

Puranjan Ghimire, Mo Motamedi, Richard Joh

Research Article | published 10 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012027

Views: 955Citations: 2Saves: 2 • Shares: 0

Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein

Timothy Hasse, Esra Mantei, Rezvan Shahoei, Shristi Pawnikar, Jinan Wang, Yinglong Miao, Yu-ming M. Huang

Research Article | published 07 Mar 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011955

Views: 989Citations: 0Saves: 0 • Shares: 0

Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation

Nadin Haase, Wolf Holtkamp, Simon Christ, Dag Heinemann, Marina V. Rodnina, Sophia Rudorf

Research Article | published 05 Mar 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011918

Views: 647Citations: 0Saves: 0 • Shares: 0

LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies

Tadeusz Satława, Mateusz Tarkowski, Sonia Wróbel, Paweł Dudzic, Tomasz Gawłowski, Tomasz Klaus, Marek Orłowski, Anna Kostyn, Sandeep Kumar, Andrew Buchanan, Konrad Krawczyk

Research Article | published 05 Mar 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011881

Views: 3433Citations: 5Saves: 0 • Shares: 0

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