Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

4,554 views
13 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

2,254 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

5,247 views
6 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

8,780 views
18 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

3,012 views

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

6,286 views
4 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

1,743 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

3,255 views
3 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

8,601 views
10 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

3,933 views
5 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

1,557 views

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

3,007 views
5 citations

Original Research

Published on 27 Jun 2023

Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex

in Biological Modeling and Simulation

Mattia Miotto
Lorenzo Di Rienzo
Greta Grassmann
Fausta Desantis
Gianluca Cidonio
Giorgio Gosti
Marco Leonetti
Giancarlo Ruocco
Edoardo Milanetti

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1205919

1,459 views
4 citations

Original Research

Published on 23 Jun 2023

Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking

in Biological Modeling and Simulation

Luis Castillo-Campos
José Luis Velázquez-Libera
Julio Caballero

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1215499

2,662 views
1 citation

Editorial

Published on 09 Jun 2023

Editorial: Web tools for modeling and analysis of biomolecular interactions Volume II

in Biological Modeling and Simulation

Jessica Andreani
Brian Jiménez-García
Masahito Ohue

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1190855

1,625 views

Original Research

Published on 31 May 2023

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation

in Biological Modeling and Simulation

Muhammad Suleman
Aneela Murtaza
Maria
Haji Khan
Farooq Rashid
Abdulrahman Alshammari
Liaqat Ali
Abbas Khan
Dong-Qing Wei

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1153046

2,973 views
10 citations

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Articles

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

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

How can we discover developable antibody-based biotherapeutics?

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

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

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

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs

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

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

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

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

Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex

Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking

Editorial: Web tools for modeling and analysis of biomolecular interactions Volume II

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation