Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

1,739 views
2 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

2,106 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

702 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

1,874 views
1 citation

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

1,952 views
3 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

1,033 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

1,824 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

2,442 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

2,214 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

1,653 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

2,054 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

3,507 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

2,322 views
1 citation

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

1,378 views
1 citation

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

2,279 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

2,235 views
1 citation