Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 01 May 2024

Deep learning-based classification of the capillary ultrastructure in human skeletal muscles

in Biological Modeling and Simulation

Marius Reto Bigler
Oliver Baum

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1363384

2,470 views

Original Research

Published on 22 Apr 2024

Analyzing molecular signatures in preeclampsia and fetal growth restriction: Identifying key genes, pathways, and therapeutic targets for preterm birth

in Biological Modeling and Simulation

Muhammad Bilal Azmi
Mushyeda Fatima Nasir
Uzma Asif
Mohsin Kazi
Mohammad N. Uddin
Shamim Akhtar Qureshi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1384214

5,367 views
4 citations

Original Research

Published on 04 Apr 2024

Chemoinformatics and machine learning techniques to identify novel inhibitors of the lemur tyrosine kinase-3 receptor involved in breast cancer

in Biological Modeling and Simulation

Faris Alrumaihi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1366763

2,180 views

Original Research

Published on 28 Mar 2024

Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications

in Biological Modeling and Simulation

Dawid Chomicz
Jarosław Kończak
Sonia Wróbel
Tadeusz Satława
Paweł Dudzic
Bartosz Janusz
Mateusz Tarkowski
Piotr Deszyński
Tomasz Gawłowski
Anna Kostyn

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1352508

11,655 views
10 citations

Original Research

Published on 28 Mar 2024

Electrophysiological properties and structural prediction of the SARS-CoV-2 viroprotein E

in Biological Modeling and Simulation

Salvatore Antonio Maria Cubisino
Stefan Milenkovic
Stefano Conti-Nibali
Nicolò Musso
Paolo Bonacci
Vito De Pinto
Matteo Ceccarelli
Simona Reina

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1334819

3,820 views
10 citations

Original Research

Published on 27 Mar 2024

Evaluation of Adenanthera pavonina-derived compounds against diabetes mellitus: insight into the phytochemical analysis and in silico assays

in Biological Modeling and Simulation

Md. Sojiur Rahman
Md. Eram Hosen
Md. Omar Faruqe
Md. Khalekuzzaman
Md. Asadul Islam
Uzzal Kumar Acharjee
Yousef A. Bin Jardan
Hiba-Allah Nafidi
Amare Bitew Mekonnen
Mohammed Bourhia

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1278701

3,593 views
3 citations

Original Research

Published on 27 Mar 2024

Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking

in Biological Modeling and Simulation

Jorge Luis Valdés-Albuernes
Erbio Díaz-Pico
Sergio Alfaro
Julio Caballero

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1374364

3,122 views
8 citations

Original Research

Published on 21 Mar 2024

An automatic diagnosis model of otitis media with high accuracy rate using transfer learning

in Biological Modeling and Simulation

Fangyu Qi
Zhiyu You
Jiayang Guo
Yongjun Hong
Xiaolong Wu
Dongdong Zhang
Qiyuan Li
Chengfu Cai

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1250596

4,233 views
1 citation

Original Research

Published on 07 Mar 2024

Integrating virtual screening, pharmacoinformatics profiling, and molecular dynamics: identification of promising inhibitors targeting 3CLpro of SARS-CoV-2

in Biological Modeling and Simulation

Abeer Mohammad
Ahmed Zheoat
Amjad Oraibi
Ajay Manaithiya
Khalid S. Almaary
Hiba Allah Nafidi
Mohammed Bourhia
Soumaya Kilani-Jaziri
Yousef A. Bin Jardan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1306179

4,327 views
1 citation

Original Research

Published on 07 Mar 2024

Revealing innovative JAK1 and JAK3 inhibitors: a comprehensive study utilizing QSAR, 3D-Pharmacophore screening, molecular docking, molecular dynamics, and MM/GBSA analyses

in Biological Modeling and Simulation

Abdelmoujoud Faris
Ivana Cacciatore
Radwan Alnajjar
Hadni Hanine
Adnane Aouidate
Ramzi A. Mothana
Abdullah R. Alanzi
Menana Elhallaoui

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1348277

8,266 views
12 citations

Original Research

Published on 01 Mar 2024

Unveiling the affinity–stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction

in Biological Modeling and Simulation

Rimpa Paul
Keisuke Kasahara
Jiei Sasaki
Jorge Fernández Pérez
Ryo Matsunaga
Takao Hashiguchi
Daisuke Kuroda
Kouhei Tsumoto

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1302737

4,773 views
1 citation

Editorial

Published on 07 Feb 2024

Editorial: Progress and challenges in computational structure-based design and development of biologic drugs

in Biological Modeling and Simulation

Traian Sulea
Sandeep Kumar
Daisuke Kuroda

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1360267

3,437 views
5 citations

Original Research

Published on 18 Jan 2024

Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2

in Biological Modeling and Simulation

José Xavier Lima Neto
Katyanna Sales Bezerra
Emmanuel Duarte Barbosa
Roniel Lima Araujo
Douglas Soares Galvão
Marcelo Leite Lyra
Jonas Ivan Nobre Oliveira
Shopnil Akash
Yousef A. Bin Jardan
Hiba-Allah Nafidi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1325588

5,021 views
5 citations

Editorial

Published on 11 Jan 2024

Editorial: Novel drug-designing approaches to combat antimicrobial resistance

in Biological Modeling and Simulation

Ghazala Muteeb
Md Tabish Rehman
Bibhusita Pani
Rizwan Hasan Khan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1342702

3,439 views
8 citations

Original Research

Published on 10 Jan 2024

Comparative transcriptomic insights into the domestication of Pleurotus abieticola for coniferous cultivation

in Biological Modeling and Simulation

Lei Sun
Frederick Leo Sossah
Yu Li
Huiying Sun

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1352163

2,158 views
1 citation

Original Research

Published on 05 Jan 2024

Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides

in Biological Modeling and Simulation

Giacomo Parisi
Roberta Piacentini
Alessio Incocciati
Alessandra Bonamore
Alberto Macone
Jakob Rupert
Elsa Zacco
Mattia Miotto
Edoardo Milanetti
Gian Gaetano Tartaglia

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1332359

5,620 views
10 citations

Original Research

Published on 29 Nov 2023

Oligomer formation of SARS-CoV-2 ORF8 through 73YIDI76 motifs regulates immune response and non-infusion antiviral interactions

in Biological Modeling and Simulation

Mohammad Assadizadeh
Maryam Azimzadeh Irani

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1270511

3,954 views
3 citations

Original Research

Published on 28 Nov 2023

Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions

in Biological Modeling and Simulation

Romain Amyot
Kaho Nakamoto
Noriyuki Kodera
Holger Flechsig

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1264161

3,748 views
5 citations

Original Research

Published on 23 Nov 2023

Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico and in vitro approaches

in Biological Modeling and Simulation

Marina Gorostiola González
Hubert J. Sijben
Laura Dall’ Acqua
Rongfang Liu
Adriaan P. IJzerman
Laura H. Heitman
Gerard J. P. van Westen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1286673

4,803 views
6 citations

Original Research

Published on 22 Nov 2023

Immunoinformatics and reverse vaccinology approach in designing a novel highly immunogenic multivalent peptide-based vaccine against the human monkeypox virus

in Biological Modeling and Simulation

Abhigyan Choudhury
Anshuman Chandra
Turki M. Dawoud
Hiba-Allah Nafidi
Nagendra Singh
Mohammed Bourhia

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1295817

4,909 views
9 citations

Original Research

Published on 22 Nov 2023

Potent VEGFR-2 inhibitors for resistant breast cancer: a comprehensive 3D-QSAR, ADMET, molecular docking and MMPBSA calculation on triazolopyrazine derivatives

in Biological Modeling and Simulation

Soukayna Baammi
Achraf El Allali
Rachid Daoud

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1288652

7,345 views
16 citations

Original Research

Published on 20 Nov 2023

Exploring potent aldose reductase inhibitors for anti-diabetic (anti-hyperglycemic) therapy: integrating structure-based drug design, and MMGBSA approaches

in Biological Modeling and Simulation

Muhammad Shahab
Guojun Zheng
Fahad M. Alshabrmi
Mohammed Bourhia
Gezahign Fentahun Wondmie
Ahmad Mohammad Salamatullah

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1271569

7,950 views
6 citations

Original Research

Published on 20 Nov 2023

Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330

in Biological Modeling and Simulation

Mutaib M. Mashraqi
Ahmad Alzamami
Norah A. Alturki
Hassan H. Almasaudi
Ibrar Ahmed
Saleh Alshamrani
Zarrin Basharat

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1258834

2,948 views
2 citations

Mini Review

Published on 10 Nov 2023

Machine learning for pan-cancer classification based on RNA sequencing data

in Biological Modeling and Simulation

Paula Štancl
Rosa Karlić

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1285795

4,881 views
9 citations

494 articles

articles

Deep learning-based classification of the capillary ultrastructure in human skeletal muscles

Analyzing molecular signatures in preeclampsia and fetal growth restriction: Identifying key genes, pathways, and therapeutic targets for preterm birth

Chemoinformatics and machine learning techniques to identify novel inhibitors of the lemur tyrosine kinase-3 receptor involved in breast cancer

Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications

Electrophysiological properties and structural prediction of the SARS-CoV-2 viroprotein E

Evaluation of Adenanthera pavonina-derived compounds against diabetes mellitus: insight into the phytochemical analysis and in silico assays

Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking

An automatic diagnosis model of otitis media with high accuracy rate using transfer learning

Integrating virtual screening, pharmacoinformatics profiling, and molecular dynamics: identification of promising inhibitors targeting 3CLpro of SARS-CoV-2

Revealing innovative JAK1 and JAK3 inhibitors: a comprehensive study utilizing QSAR, 3D-Pharmacophore screening, molecular docking, molecular dynamics, and MM/GBSA analyses

Unveiling the affinity–stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction

Editorial: Progress and challenges in computational structure-based design and development of biologic drugs

Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2

Editorial: Novel drug-designing approaches to combat antimicrobial resistance

Comparative transcriptomic insights into the domestication of Pleurotus abieticola for coniferous cultivation

Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides

Oligomer formation of SARS-CoV-2 ORF8 through 73YIDI76 motifs regulates immune response and non-infusion antiviral interactions

Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions

Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico and in vitro approaches

Immunoinformatics and reverse vaccinology approach in designing a novel highly immunogenic multivalent peptide-based vaccine against the human monkeypox virus

Potent VEGFR-2 inhibitors for resistant breast cancer: a comprehensive 3D-QSAR, ADMET, molecular docking and MMPBSA calculation on triazolopyrazine derivatives

Exploring potent aldose reductase inhibitors for anti-diabetic (anti-hyperglycemic) therapy: integrating structure-based drug design, and MMGBSA approaches

Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330

Machine learning for pan-cancer classification based on RNA sequencing data