Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

4,101 views
3 citations

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

6,167 views
13 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

1,963 views
5 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

3,499 views
2 citations

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

14,397 views
20 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

17,986 views
24 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

2,860 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

7,099 views
24 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

7,711 views
28 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

2,463 views
3 citations

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

4,339 views
3 citations

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

3,926 views
5 citations

Original Research

Published on 10 Aug 2023

Anti-quorum sensing potential of selenium nanoparticles against LasI/R, RhlI/R, and PQS/MvfR in Pseudomonas aeruginosa: a molecular docking approach

in Biological Modeling and Simulation

Kanak Raj Kanak
Regina Sharmila Dass
Archana Pan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1203672

7,474 views
27 citations

Original Research

Published on 10 Aug 2023

Genetic analysis of acute intermittent porphyria caused by novel classical splicing variant in the insertion region of 29-residue specific to human HMBS protein

in Biological Modeling and Simulation

Lei Liang
Haixia Meng
Haotian Wu
Jianrong Zhao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1230798

3,268 views

Original Research

Published on 09 Aug 2023

In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria

in Biological Modeling and Simulation

Harpreet Singh
Shaikha Y. Almaazmi
Tanima Dutta
Robert A. Keyzers
Gregory L. Blatch

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1158912

8,384 views
8 citations

Review

Published on 07 Aug 2023

How can we discover developable antibody-based biotherapeutics?

in Biological Modeling and Simulation

Joschka Bauer
Nandhini Rajagopal
Priyanka Gupta
Pankaj Gupta
Andrew E. Nixon
Sandeep Kumar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1221626

12,982 views
27 citations

Original Research

Published on 04 Aug 2023

Machine learning-driven exploration of drug therapies for triple-negative breast cancer treatment

in Biological Modeling and Simulation

Aman Chandra Kaushik
Zhongming Zhao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1215204

4,644 views
2 citations

Hypothesis and Theory

Published on 25 Jul 2023

Integrated immunoinformatics and subtractive proteomics approach for multi-epitope vaccine designing to combat S. pneumoniae TIGR4

in Biological Modeling and Simulation

Sami S. Ashgar
Hani Faidah
Farkad Bantun
Naif A. Jalal
Naeem F. Qusty
Abdulla Darwish
Shafiul Haque
Essam M. Janahi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1212119

7,922 views
9 citations

Original Research

Published on 14 Jul 2023

A stochastic B cell affinity maturation model to characterize mechanisms of protection for tetravalent dengue vaccine constructs

in Biological Modeling and Simulation

Venkat R. Pannala
Hung D. Nguyen
Anders Wallqvist

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1100434

2,410 views

Review

Published on 11 Jul 2023

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs

in Biological Modeling and Simulation

Zeyaul Islam
Pankaj Kumar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1228763

6,532 views
12 citations

Mini Review

Published on 07 Jul 2023

Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery

in Biological Modeling and Simulation

Igor Jaszczyszyn
Weronika Bielska
Tomasz Gawlowski
Pawel Dudzic
Tadeusz Satława
Jarosław Kończak
Wiktoria Wilman
Bartosz Janusz
Sonia Wróbel
Dawid Chomicz

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1214424

10,938 views
16 citations

Brief Research Report

Published on 30 Jun 2023

SMG-BERT: integrating stereoscopic information and chemical representation for molecular property prediction

in Biological Modeling and Simulation

Jiahui Zhang
Wenjie Du
Xiaoting Yang
Di Wu
Jiahe Li
Kun Wang
Yang Wang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1216765

5,431 views
12 citations

Original Research

Published on 27 Jun 2023

Hybrid neural network approaches to predict drug–target binding affinity for drug repurposing: screening for potential leads for Alzheimer’s disease

in Biological Modeling and Simulation

Xialin Wu
Zhuojian Li
Guanxing Chen
Yiyang Yin
Calvin Yu-Chian Chen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1227371

5,235 views
10 citations

Original Research

Published on 27 Jun 2023

Variability of the innate immune response is globally constrained by transcriptional bursting

in Biological Modeling and Simulation

Nissrin Alachkar
Dale Norton
Zsofia Wolkensdorfer
Mark Muldoon
Pawel Paszek

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1176107

3,022 views
3 citations