Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

2,907 views
2 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

2,772 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

1,992 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

2,521 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

1,514 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

3,120 views
3 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

1,079 views
4 citations

Original Research

Published on 11 Oct 2023

Developmental landscape of computational techniques to explore the potential phytochemicals from Punica granatum peels for their antioxidant activity in Alzheimer’s disease

in Biological Modeling and Simulation

Shagufta Parveen
Aneeqa Batool
Nusrat Shafiq
Maryam Rashid
Ayesha Sultan
Gezahign Fentahun Wondmie
Yousef A. Bin Jardan
Simone Brogi
Mohammed Bourhia

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1252178

2,436 views

Methods

Published on 10 Oct 2023

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina

in Biological Modeling and Simulation

Fabian Krause
Karsten Voigt
Barbara Di Ventura
Mehmet Ali Öztürk

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1243970

7,821 views
2 citations

Original Research

Published on 28 Sep 2023

AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study

in Biological Modeling and Simulation

Paul Arras
Han Byul Yoo
Lukas Pekar
Thomas Clarke
Lukas Friedrich
Christian Schröter
Jennifer Schanz
Jason Tonillo
Vanessa Siegmund
Achim Doerner

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1249247

11,137 views
7 citations

Original Research

Published on 27 Sep 2023

Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping

in Biological Modeling and Simulation

Masaud Shah
Hyun Goo Woo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1236617

1,810 views
3 citations

Original Research

Published on 20 Sep 2023

Unleashing Nature’s potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations

in Biological Modeling and Simulation

Soukayna Baammi
Achraf El Allali
Rachid Daoud

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1227643

3,761 views
7 citations

Original Research

Published on 18 Sep 2023

Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope

in Biological Modeling and Simulation

Fabian C. Spoendlin
Brennan Abanades
Matthew I. J. Raybould
Wing Ki Wong
Guy Georges
Charlotte M. Deane

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1237621

4,791 views
12 citations

Original Research

Published on 18 Sep 2023

Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes

in Biological Modeling and Simulation

Beste Ozaydin
Carles Curutchet

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1268278

1,482 views

Original Research

Published on 18 Sep 2023

Hierarchical machine learning model predicts antimicrobial peptide activity against Staphylococcus aureus

in Biological Modeling and Simulation

Hosein Khabaz
Mehdi Rahimi-Nasrabadi
Amir Homayoun Keihan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1238509

1,897 views
1 citation

Original Research

Published on 24 Aug 2023

Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold

in Biological Modeling and Simulation

Francis Gaudreault
Jason Baardsnes
Yuliya Martynova
Aurore Dachon
Hervé Hogues
Christopher R. Corbeil
Enrico O. Purisima
Mélanie Arbour
Traian Sulea

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1253689

2,257 views
2 citations

Navigation group

Articles

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

Developmental landscape of computational techniques to explore the potential phytochemicals from Punica granatum peels for their antioxidant activity in Alzheimer’s disease

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina

AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study

Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping

Unleashing Nature’s potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations

Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope

Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes

Hierarchical machine learning model predicts antimicrobial peptide activity against Staphylococcus aureus

Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold