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

8,022 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

3,688 views
4 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

1,430 views
1 citation

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

1,326 views
3 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

2,731 views
2 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

2,523 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

1,562 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

2,759 views
6 citations

Original Research

Published on 18 May 2023

Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes

in Biological Modeling and Simulation

Hengyi Xie
Harel Weinstein

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1197154

3,649 views
3 citations

Technology and Code

Published on 09 May 2023

Guiding protein design choices by per-residue energy breakdown analysis with an interactive web application

in Biological Modeling and Simulation

Felipe Engelberger
Jonathan D. Zakary
Georg Künze

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1178035

2,384 views
1 citation

Editorial

Published on 27 Apr 2023

Editorial: In Celebration of Women in Science: Biological Modeling and Simulation

in Biological Modeling and Simulation

Burcu Aykac Fas
Sophie Sacquin-Mora
Elena Papaleo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1175325

2,472 views

Original Research

Published on 21 Apr 2023

Identification of fungus-growing termite-associated halogenated-PKS maduralactomycin a as a potential inhibitor of MurF protein of multidrug-resistant Acinetobacter baumannii

in Biological Modeling and Simulation

Muhammad Shoaib
Iram Shehzadi
Muhammad Umair Asif
Yulong Shen
Jinfeng Ni

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1183073

1,947 views
1 citation

Original Research

Published on 18 Apr 2023

Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors

in Biological Modeling and Simulation

Artur Meller
Saulo De Oliveira
Aram Davtyan
Tigran Abramyan
Gregory R. Bowman
Henry van den Bedem

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1171143

6,889 views
9 citations

Original Research

Published on 07 Mar 2023

Identification of novel inhibitors for SARS-CoV-2 as therapeutic options using machine learning-based virtual screening, molecular docking and MD simulation

in Biological Modeling and Simulation

Abdus Samad
Amar Ajmal
Arif Mahmood
Beenish Khurshid
Ping Li
Syed Mansoor Jan
Ashfaq Ur Rehman
Pei He
Ashraf N. Abdalla
Muhammad Umair

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1060076

5,055 views
35 citations

Original Research

Published on 03 Mar 2023

Homology modeling, virtual screening, molecular docking, and dynamics studies for discovering Staphylococcus epidermidis FtsZ inhibitors

in Biological Modeling and Simulation

Divya Vemula
Dhanashri Ramesh Maddi
Vasundhra Bhandari

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1087676

5,236 views
7 citations

Original Research

Published on 02 Mar 2023

Computational design of fusion proteins against ErbB2-amplified tumors inspired by ricin toxin

in Biological Modeling and Simulation

Yasser Ahmadi Moghaddam
Asad Maroufi
Sara Zareei
Mehdi Irani

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1098365

2,322 views
4 citations

Navigation group

Articles

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

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

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

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

Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes

Guiding protein design choices by per-residue energy breakdown analysis with an interactive web application

Editorial: In Celebration of Women in Science: Biological Modeling and Simulation

Identification of fungus-growing termite-associated halogenated-PKS maduralactomycin a as a potential inhibitor of MurF protein of multidrug-resistant Acinetobacter baumannii

Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors

Identification of novel inhibitors for SARS-CoV-2 as therapeutic options using machine learning-based virtual screening, molecular docking and MD simulation

Homology modeling, virtual screening, molecular docking, and dynamics studies for discovering Staphylococcus epidermidis FtsZ inhibitors

Computational design of fusion proteins against ErbB2-amplified tumors inspired by ricin toxin