Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

3,787 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

2,706 views
2 citations

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

2,543 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

2,207 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

7,477 views
11 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

5,596 views
45 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

5,996 views
14 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

2,616 views
5 citations

Original Research

Published on 01 Mar 2023

PROT-ON: A structure-based detection of designer PROTein interface MutatiONs

in Biological Modeling and Simulation

Mehdi Koşaca
İrem Yılmazbilek
Ezgi Karaca

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1063971

4,419 views
2 citations

Original Research

Published on 23 Feb 2023

Ligand-based pharmacophore modeling and QSAR approach to identify potential dengue protease inhibitors

in Biological Modeling and Simulation

Anushka A. Poola
Prithvi S. Prabhu
T. P. Krishna Murthy
Manikanta Murahari
Swati Krishna
Mahesh Samantaray
Amutha Ramaswamy

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1106128

3,805 views
7 citations

Brief Research Report

Published on 16 Feb 2023

Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties

in Biological Modeling and Simulation

Davide Sala
Peter W. Hildebrand
Jens Meiler

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1121962

8,047 views
49 citations

Original Research

Published on 14 Feb 2023

Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection

in Biological Modeling and Simulation

Ahmed M. Gouda
Mohamed A. Soltan
Khalid Abd-Elghany
Ashraf E. Sileem
Hanan M. Elnahas
Marwa Abdel-Monem Ateya
Mahmoud H. Elbatreek
Khaled M. Darwish
Hanin A. Bogari
Manar O. Lashkar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1123411

7,158 views
12 citations

Original Research

Published on 09 Feb 2023

Coupled binding and folding of disordered SPIN N-terminal region in myeloperoxidase inhibition

in Biological Modeling and Simulation

Yumeng Zhang
Xiaorong Liu
Jianhan Chen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1130189

2,152 views
3 citations

Original Research

Published on 09 Feb 2023

In-silico drug design for the novel Karachi-NF001 strain of brain-eating amoeba: Naegleria fowleri

in Biological Modeling and Simulation

Tayyab Saleem
Syed Babar Jamal
Badr Alzahrani
Amina Basheer
Sumra Wajid Abbasi
Mahwish Ali
Ashfaq Ur Rehman
Muhammad Faheem

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1098217

6,765 views
4 citations

Original Research

Published on 26 Jan 2023

Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides

in Biological Modeling and Simulation

Kevin J. González-Morelo
Edgardo Galán-Vásquez
Felipe Melis
Ernesto Pérez-Rueda
Daniel Garrido

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1040721

4,055 views
3 citations

Editorial

Published on 24 Jan 2023

Editorial: Biomolecular function and activity modulated by membranes

in Biological Modeling and Simulation

Giray Enkavi
Jing Li
Hector Martinez-Seara

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1133034

1,831 views

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Articles

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

PROT-ON: A structure-based detection of designer PROTein interface MutatiONs

Ligand-based pharmacophore modeling and QSAR approach to identify potential dengue protease inhibitors

Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties

Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection

Coupled binding and folding of disordered SPIN N-terminal region in myeloperoxidase inhibition

In-silico drug design for the novel Karachi-NF001 strain of brain-eating amoeba: Naegleria fowleri

Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides

Editorial: Biomolecular function and activity modulated by membranes