Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

8,249 views
8 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

2,796 views
7 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

2,369 views
2 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

1,989 views
3 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

2,157 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

3,089 views

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

5,295 views
7 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

3,610 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

2,277 views
4 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

3,395 views
3 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

2,435 views
6 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

1,412 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

3,873 views
5 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

3,050 views
2 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

2,618 views
4 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

3,385 views
4 citations