Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

Review

Accepted on 17 Mar 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

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

191 views

Original Research

Accepted on 05 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

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

673 views

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

552 views

Original Research

Accepted on 24 Feb 2025

Successful prediction of LC8 binding to intrinsically disordered proteins illuminates AlphaFold's black box

in Biological Modeling and Simulation

Douglas R Walker
Gretchen Fujimura
Juan M Vanegas
Elisar Barbar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1531793

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

751 views

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

511 views

Original Research

Published on 29 Jan 2025

Individual-network based predictions of microbial interaction signatures for response to biological therapies in IBD patients

in Biological Modeling and Simulation

Federico Melograna
Padhmanand Sudhakar
Behnam Yousefi
Clara Caenepeel
Gwen Falony
Sara Vieira-Silva
Sreenikhitha Krishnamoorthy
David Fardo
Bram Verstockt
Jeroen Raes

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1490533

1,462 views

Original Research

Published on 23 Jan 2025

Linking machine learning and biophysical structural features in drug discovery

in Biological Modeling and Simulation

Armin Ahmadi
Shivangi Gupta
Vineetha Menon
Jerome Baudry

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1305272

1,025 views

Editorial

Published on 03 Jan 2025

Editorial: Revolutionizing life sciences: the nobel leap in artificial intelligence-driven biomodeling

in Biological Modeling and Simulation

Valentina Tozzini
Cecilia Giulivi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1540823

926 views

Original Research

Published on 02 Dec 2024

Exploring TAS2R46 biomechanics through molecular dynamics and network analysis

in Biological Modeling and Simulation

Marco Cannariato
Riccardo Fanunza
Eric A. Zizzi
Marcello Miceli
Giacomo Di Benedetto
Marco A. Deriu
Lorenzo Pallante

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1473675

1,139 views

Original Research

Published on 14 Nov 2024

Protein-free domains in native and ferroptosis-driven oxidized cell membranes: a molecular dynamics study of biophysical properties and doxorubicin uptake

in Biological Modeling and Simulation

Yaser Shabanpour
Behnam Hajipour-Verdom
Parviz Abdolmaleki
Mozhgan Alipour

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1494257

944 views

Original Research

Published on 09 Oct 2024

Exploration of phytoconstituents of Medhya Rasayana herbs to identify potential inhibitors for cerebroside sulfotransferase through high-throughput screening

in Biological Modeling and Simulation

Nivedita Singh
Anil Kumar Singh

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1476482

1,350 views
1 citation

Correction

Published on 04 Oct 2024

Corrigendum: Deepening insights into cholinergic agents for intraocular pressure reduction: systems genetics, molecular modeling, and in vivo perspectives

in Biological Modeling and Simulation

Minjae J. Kim
Mohamed M. Ibrahim
Monica M. Jablonski

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1490100

519 views

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Articles

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

Use of AI-Methods over MD Simulations in the Sampling of Conformational Ensembles in IDPs

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

Computational Analysis of the Structural-Functional Dynamics of a Co-receptor proteoglycan

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

Editorial: Machine learning in computer-aided drug design

Successful prediction of LC8 binding to intrinsically disordered proteins illuminates AlphaFold's black box

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

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

Individual-network based predictions of microbial interaction signatures for response to biological therapies in IBD patients

Linking machine learning and biophysical structural features in drug discovery

Editorial: Revolutionizing life sciences: the nobel leap in artificial intelligence-driven biomodeling

Exploring TAS2R46 biomechanics through molecular dynamics and network analysis

Protein-free domains in native and ferroptosis-driven oxidized cell membranes: a molecular dynamics study of biophysical properties and doxorubicin uptake

Exploration of phytoconstituents of Medhya Rasayana herbs to identify potential inhibitors for cerebroside sulfotransferase through high-throughput screening

Corrigendum: Deepening insights into cholinergic agents for intraocular pressure reduction: systems genetics, molecular modeling, and in vivo perspectives