Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

297 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

235 views

Editorial

Accepted on 03 Feb 2025

Machine Learning in Computer-Aided Drug DesignEditorial

in Biological Modeling and Simulation

Ognjen Perisic
Cigdem Sevim Bayrak
Mohamed Khaled Gunady

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2025.1568437

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

608 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

688 views

Brief Research Report

Accepted on 13 Jan 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

118 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

748 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

836 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

779 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

1,253 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

448 views

Original Research

Published on 10 Sep 2024

From in vitro to in silico: a pipeline for generating virtual tissue simulations from real image data

in Biological Modeling and Simulation

Elina Nürnberg
Mario Vitacolonna
Roman Bruch
Markus Reischl
Rüdiger Rudolf
Simeon Sauer

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1467366

1,176 views

Original Research

Published on 06 Sep 2024

A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis

in Biological Modeling and Simulation

Asma Fatima
Anupriya M. Geethakumari
Wesam S. Ahmed
Kabir H. Biswas

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1451280

1,197 views
1 citation

Original Research

Published on 05 Sep 2024

LncSTPred: a predictive model of lncRNA subcellular localization and decipherment of the biological determinants influencing localization

in Biological Modeling and Simulation

Si-Le Hu
Ying-Li Chen
Lu-Qiang Zhang
Hui Bai
Jia-Hong Yang
Qian-Zhong Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1452142

624 views
1 citation

Original Research

Published on 13 Aug 2024

Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants

in Biological Modeling and Simulation

Sara AlRawashdeh
Farag E. S. Mosa
Khaled H. Barakat

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1341727

1,207 views

Original Research

Published on 09 Aug 2024

Structural modifications and kinetic effects of KRAS interactions with HRAS and NRAS: an in silico comparative analysis of KRAS mutants

in Biological Modeling and Simulation

Isaac Silverman
Michael Gerber
Aaron Shaykevich
Yitzchak Stein
Alexander Siegman
Sanjay Goel
Radhashree Maitra

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1436976

1,696 views

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Articles

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

Machine Learning in Computer-Aided Drug DesignEditorial

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

Uncovering a Novel Binding Trench in ERRα: Insights from Molecular Simulations

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

From in vitro to in silico: a pipeline for generating virtual tissue simulations from real image data

A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis

LncSTPred: a predictive model of lncRNA subcellular localization and decipherment of the biological determinants influencing localization

Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants

Structural modifications and kinetic effects of KRAS interactions with HRAS and NRAS: an in silico comparative analysis of KRAS mutants