Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 03 Sep 2025

Local sequence context at KRAS codons modulates DNA repair efficiency: insights from molecular dynamics simulations

in Biological Modeling and Simulation

James Davies
Georgina E. Menzies

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1654434

431 views

Original Research

Accepted on 26 Aug 2025

SRC Is a Potential Target of Arctigenin in Treating Triple-Negative Breast Cancer: Based on Machine Learning Algorithms, Molecular Modeling and in Vitro Test

in Biological Modeling and Simulation

Tianping Li
Yuezhou Huang
Qing Luo
Linfeng Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1644169

317 views

Original Research

Accepted on 22 Aug 2025

Role of Intercellular Interactions on Single Cell and Population Level Responses: Considerations for Multicellular Bioreporter Design

in Biological Modeling and Simulation

Douglas Lin
Michael Martin

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1595363

330 views

Brief Research Report

Published on 13 Aug 2025

Modelling the melting of DNA oligomers with non-inert dangling ends

in Biological Modeling and Simulation

Alejandro Soto
Francesco Mambretti
Emanuele Locatelli
Iliya D. Stoev

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1646428

1,327 views

Original Research

Published on 11 Jul 2025

Integrating multi-dimensional data to reveal the mechanisms and molecular targets of baikening granules for treatment of pediatric influenza

in Biological Modeling and Simulation

Zhaoyuan Gong
Qianzi Che
Mingzhi Hu
Tian Song
Lin Chen
Haili Zhang
Ning Liang
Huizhen Li
Guozhen Zhao
Lijiao Yan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1637980

1,698 views

Correction

Published on 19 May 2025

Corrigendum: Computational analysis of the structural-functional dynamics of a Co-receptor proteoglycan

in Biological Modeling and Simulation

Francesco Tavanti
Giorgia Brancolini
Roberto Perris

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1612818

783 views

Original Research

Published on 06 May 2025

Exploring focal adhesion data: dynamic parameter extraction from FRAP and FLAP experiments using chemical master equation

in Biological Modeling and Simulation

Luciana Renata de Oliveira
Matheus Gimenez Fernandes
José Salvatore Leister Patane
Jean-Marc Schwartz
José Eduardo Krieger
Christoph Ballestrem
Ayumi Aurea Miyakawa

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1587608

1,555 views

Original Research

Published on 23 Apr 2025

Successful prediction of LC8 binding to intrinsically disordered proteins sheds light on AlphaFold’s black box

in Biological Modeling and Simulation

Douglas R. Walker
Gretchen Fujimura
Juan M. Vanegas
Elisar J. Barbar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1531793

2,682 views
1 citation

Review

Published on 08 Apr 2025

Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs

in Biological Modeling and Simulation

Souradeep Sil
Ishita Datta
Sankar Basu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1542267

3,952 views
1 citation

Original Research

Published on 25 Mar 2025

Computational analysis of the structural-functional dynamics of a Co-receptor proteoglycan

in Biological Modeling and Simulation

Francesco Tavanti
Giorgia Brancolini
Roberto Perris

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1549177

1,795 views

Original Research

Published on 19 Mar 2025

Computational molecular insights into ibrutinib as a potent inhibitor of HER2-L755S mutant in breast cancer: gene expression studies, virtual screening, docking, and molecular dynamics analysis

in Biological Modeling and Simulation

Tamizhini Loganathan
C. George Priya Doss

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1510896

2,782 views

Review

Published on 17 Mar 2025

Exploring chemical space for “druglike” small molecules in the age of AI

in Biological Modeling and Simulation

Aman Achuthan Kattuparambil
Dheeraj Kumar Chaurasia
Shashank Shekhar
Ashwin Srinivasan
Sukanta Mondal
Raviprasad Aduri
B. Jayaram

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1553667

2,554 views
1 citation

Brief Research Report

Published on 27 Feb 2025

Uncovering a novel binding trench in ERRα: insights from molecular simulations

in Biological Modeling and Simulation

Lamees Hegazy

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1523932

2,051 views
1 citation

Editorial

Published on 25 Feb 2025

Editorial: Machine learning in computer-aided drug design

in Biological Modeling and Simulation

Ognjen Perišić
Cigdem Sevim Bayrak
Mohamed Khaled Gunady

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1568437

1,391 views

Original Research

Published on 14 Feb 2025

Metabolite profiling, antimalarial potentials of Schleichera oleosa using LC-MS and GC-MS: in vitro, molecular docking and molecular dynamics

in Biological Modeling and Simulation

Peetha Vanaja
N. S. Hari Narayana Moorthy
Vivek Singh Rajpoot
Harshawardhan Rao
Rohit Kumar Goswami
Paranthaman Subash
Sulekha Khute
Kareti Srinivasa Rao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1543939

3,699 views
3 citations

Original Research

Published on 11 Feb 2025

Simulations of pH and thermal effects on SARS-CoV-2 spike glycoprotein

in Biological Modeling and Simulation

Ziyuan Niu
Georgios Kementzidis
Miriam Rafailovich
Marcia Simon
Evangelos Papadopoulos
Bertal H. Aktas
Yuefan Deng

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1545041

1,511 views
2 citations