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

1,722 views
1 citation

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

2,381 views
1 citation

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

1,591 views
3 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

1,039 views

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

2,881 views
2 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

2,438 views
1 citation

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

2,013 views
2 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

2,565 views
3 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

2,249 views
3 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

2,468 views
1 citation

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

2,057 views
2 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

1,726 views

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

2,132 views

Original Research

Published on 06 Nov 2023

Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes

in Biological Modeling and Simulation

Lei Sun
Xiaolei Yin
Frederick Leo Sossah
Xuerong Han
Yu Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1292556

1,345 views

Original Research

Published on 30 Oct 2023

Antibacterial and antibiofilm activity of Abroma augusta stabilized silver (Ag) nanoparticles against drug-resistant clinical pathogens

in Biological Modeling and Simulation

Sachin Kumar
Haris M. Khan
Fohad Mabood Husain
Rafiq Ahmad
Faizan Abul Qais
Mo Ahamad Khan
Mohammad Jalal
Uzma Tayyaba
Syed Ghazanfar Ali
Amardeep Singh

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1292509

2,476 views
2 citations

Methods

Published on 24 Oct 2023

ReDirection: an R-package to compute the probable dissociation constant for every reaction of a user-defined biochemical network

in Biological Modeling and Simulation

Siddhartha Kundu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1206502

967 views
4 citations

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Articles

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

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

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

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

Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes

Antibacterial and antibiofilm activity of Abroma augusta stabilized silver (Ag) nanoparticles against drug-resistant clinical pathogens

ReDirection: an R-package to compute the probable dissociation constant for every reaction of a user-defined biochemical network