Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

4,612 views
2 citations

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

3,295 views
1 citation

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

2,560 views
1 citation

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

3,174 views
3 citations

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

3,043 views
4 citations

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

3,216 views
2 citations

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

1,129 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

3,227 views
3 citations

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

3,455 views
7 citations

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

1,654 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

2,714 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

4,128 views
4 citations

Original Research

Published on 07 Aug 2024

Discovery of an 8-oxoguanine regulator PCBP1 inhibitor by virtual screening and its synergistic effects with ROS-modulating agents in pancreatic cancer

in Biological Modeling and Simulation

Kexiong Qiao
Chengjie Xu
Chaolei Zhang
Qianqian Wang
Jun Jiang
Zongrong Chen
Liangjing Zhou
Shengnan Jia
Liping Cao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1441550

3,463 views
2 citations

Original Research

Published on 05 Aug 2024

Molecular dynamic simulation reveals the inhibiting impact of Rhein on wild-type and P29S-mutated Rac1

in Biological Modeling and Simulation

Negar Etebar
Seyed Hootan Hamidi
Saghi Naderpour
Omar Abouali
Seyedeh Harir Hamidi
Behnam Hajipour-Verdom
Alireza Zali
Mozhgan Alipour
Milad Rahimzadegan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1414197

2,517 views

Methods

Published on 01 Aug 2024

Innovative tree-based method for sampling molecular conformations: exploring the ATP-binding cassette subfamily D member 1 (ABCD1) transporter as a case study

in Biological Modeling and Simulation

Thomas Haschka
Foudil Lamari
Fanny Mochel
Violetta Zujovic

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1440529

2,877 views

Original Research

Published on 26 Jul 2024

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.2024.1423351

6,521 views

Original Research

Published on 11 Jul 2024

Bibliometric analysis on CRISPR/Cas: a potential Sherlock Holmes for disease detection

in Biological Modeling and Simulation

Rohan Samir Kumar Sachan
Adarsh Choudhary
Inderpal Devgon
Arun Karnwal
Abdel Rahman Mohammad Said Al-Tawaha
Tabarak Malik

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1383268

3,511 views
2 citations

Original Research

Published on 13 Jun 2024

Evaluation of the clinical value of 10 estimating glomerular filtration rate equations and construction of a prediction model for kidney damage in adults from central China

in Biological Modeling and Simulation

Xian Wang
Xingcheng Xu
Yongsheng Wang
Lei Liu
Ying Xu
Jun Liu
Benjin Hu
Xiaowei Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1408503

2,301 views
2 citations

Original Research

Published on 12 Jun 2024

Computational design and investigation of the monomeric spike SARS-CoV-2-ferritin nanocage vaccine stability and interactions

in Biological Modeling and Simulation

Farnaz Garmeh Motlagh
Maryam Azimzadeh Irani
Seyedeh Zeinab Masoomi Nomandan
Mohammad Assadizadeh

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1403635

3,571 views
2 citations

Original Research

Published on 11 Jun 2024

Active and machine learning-enhanced discovery of new FGFR3 inhibitor, Rhapontin, through virtual screening of receptor structures and anti-cancer activity assessment

in Biological Modeling and Simulation

Qingxin Zeng
Haichuan Hu
Zhengwei Huang
Aotian Guo
Sheng Lu
Wenbin Tong
Zhongheng Zhang
Tao Shen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1413214

3,583 views
3 citations

Original Research

Published on 10 Jun 2024

Mechanistic insight into the mode of inhibition of dietary flavonoids; targeting macrophage migration inhibitory factor

in Biological Modeling and Simulation

Ali Raza Siddiqui
Mamona Mushtaq
Madiha Sardar
Lubna Atta
Mohammad Nur-e-Alam
Aftab Ahmad
Zaheer Ul-Haq

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1414572

3,071 views
3 citations

Original Research

Published on 28 May 2024

Identification of the inhibition mechanism of carbonic anhydrase II by fructooligosaccharides

in Biological Modeling and Simulation

Yue Mu
Qingyang Meng
Xinyi Fan
Shuyun Xi
Zhongli Xiong
Yihua Wang
Yanling Huang
Zhen Liu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1398603

3,266 views
5 citations

Original Research

Published on 24 May 2024

Study of hub nodes of transcription factor-target gene regulatory network and immune mechanism for type 2 diabetes based on chip analysis of GEO database

in Biological Modeling and Simulation

Guangyu Xu
Yuehan Zhao
Yu Bai
Yan Lin

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1410004

2,745 views
2 citations

Original Research

Published on 06 May 2024

The bioelectric mechanisms of local calcium dynamics in cancer cell proliferation: an extension of the A549 in silico cell model

in Biological Modeling and Simulation

Sonja Langthaler
Christian Zumpf
Theresa Rienmüller
Niroj Shrestha
Julia Fuchs
Rui Zhou
Brigitte Pelzmann
Klaus Zorn-Pauly
Eleonore Fröhlich
Seth H. Weinberg

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1394398

3,722 views
3 citations

494 articles

articles

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

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

Discovery of an 8-oxoguanine regulator PCBP1 inhibitor by virtual screening and its synergistic effects with ROS-modulating agents in pancreatic cancer

Molecular dynamic simulation reveals the inhibiting impact of Rhein on wild-type and P29S-mutated Rac1

Innovative tree-based method for sampling molecular conformations: exploring the ATP-binding cassette subfamily D member 1 (ABCD1) transporter as a case study

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

Bibliometric analysis on CRISPR/Cas: a potential Sherlock Holmes for disease detection

Evaluation of the clinical value of 10 estimating glomerular filtration rate equations and construction of a prediction model for kidney damage in adults from central China

Computational design and investigation of the monomeric spike SARS-CoV-2-ferritin nanocage vaccine stability and interactions

Active and machine learning-enhanced discovery of new FGFR3 inhibitor, Rhapontin, through virtual screening of receptor structures and anti-cancer activity assessment

Mechanistic insight into the mode of inhibition of dietary flavonoids; targeting macrophage migration inhibitory factor

Identification of the inhibition mechanism of carbonic anhydrase II by fructooligosaccharides

Study of hub nodes of transcription factor-target gene regulatory network and immune mechanism for type 2 diabetes based on chip analysis of GEO database

The bioelectric mechanisms of local calcium dynamics in cancer cell proliferation: an extension of the A549 in silico cell model