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mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data.

• Authors : Pérez-Hernández G; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.; Hildebrand PW

Subjects: Molecular Dynamics Simulation* ; Software* ; Computational Biology*/Computational Biology*/Computational Biology*/methods

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 21; Vol. 21 (4), pp. e1012837. Date of Electronic Publication: 2025 Apr 21 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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

• Authors : Bayarri G; Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain.; Andrio P

Subjects: Software* ; Molecular Dynamics Simulation* ; Workflow*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jun 20; Vol. 20 (6), pp. e1012173. Date of Electronic Publication: 2024 Jun 20 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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

• Authors : Jiang H; College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China.; Xu Y

Subjects: RNA, Circular*/RNA, Circular*/RNA, Circular*/chemistry ; RNA, Circular*/RNA, Circular*/RNA, Circular*/genetics ; Molecular Dynamics Simulation*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Oct 28; Vol. 20 (10), pp. e1012293. Date of Electronic Publication: 2024 Oct 28 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.

• Authors : Rocha U; Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany.; Kasmanas JC

Subjects: Metagenome*/Metagenome*/Metagenome*/genetics ; Microbiota*/Microbiota*/Microbiota*/genetics ; Computer Simulation*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Oct 22; Vol. 20 (10), pp. e1012530. Date of Electronic Publication: 2024 Oct 22 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.

• Authors : Ferraz MVF; Department of virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil.; Department of fundamental chemistry, Federal University of Pernambuco, Recife, Brazil.

Subjects: Spike Glycoprotein, Coronavirus*/Spike Glycoprotein, Coronavirus*/Spike Glycoprotein, Coronavirus*/immunology ; Spike Glycoprotein, Coronavirus*/Spike Glycoprotein, Coronavirus*/Spike Glycoprotein, Coronavirus*/chemistry ; Machine Learning*

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 21; Vol. 21 (4), pp. e1012921. Date of Electronic Publication: 2025 Apr 21 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays.

• Authors : Jin Z; Department of Colorectal Surgery and Oncology of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.; Zhou X

Subjects: Gene Regulatory Networks*/Gene Regulatory Networks*/Gene Regulatory Networks*/genetics ; Models, Biological*; Stochastic Processes

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 08; Vol. 21 (4), pp. e1012919. Date of Electronic Publication: 2025 Apr 08 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution.

• Authors : Dinh KN; Irving Institute for Cancer Dynamics, Columbia University, New York, New York, United States of America.; Department of Statistics, Columbia University, New York, New York, United States of America.

Subjects: Chromosomal Instability*/Chromosomal Instability*/Chromosomal Instability*/genetics ; Neoplasms*/Neoplasms*/Neoplasms*/genetics ; Single-Cell Analysis*/Single-Cell Analysis*/Single-Cell Analysis*/methods

• Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 03; Vol. 21 (4), pp. e1012902. Date of Electronic Publication: 2025 Apr 03 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference.

• Authors : Tolley, Nicholas¹ (AUTHOR) ; Rodrigues, Pedro L. C.² (AUTHOR); Gramfort, Alexandre³ (AUTHOR)

• Source: PLoS Computational Biology. 2/26/2024, Vol. 20 Issue 2, p1-29. 29p.

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Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment.

• Authors : Leech V; Department of Mathematics, University College London, London, United Kingdom.; Kenny FN

Subjects: Cytoskeleton*/Cytoskeleton*/Cytoskeleton*/physiology ; Intercellular Junctions*/Intercellular Junctions*/Intercellular Junctions*/physiology ; Models, Biological*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jul 29; Vol. 20 (7), pp. e1011879. Date of Electronic Publication: 2024 Jul 29 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate.

• Authors : Chiang H; Department of Mechanical Engineering, National Central University, Taoyuan, Taiwan.; Chung CA

Subjects: Vascular Endothelial Growth Factor A*/Vascular Endothelial Growth Factor A*/Vascular Endothelial Growth Factor A*/metabolism ; Capillaries*/Capillaries*/Capillaries*/metabolism ; Computer Simulation*

• Source: PLoS computational biology [PLoS Comput Biol] 2024 Jul 22; Vol. 20 (7), pp. e1012281. Date of Electronic Publication: 2024 Jul 22 (Print Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet

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