Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

2,447 views
7 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

4,132 views
4 citations

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

2,171 views
1 citation

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

4,128 views
17 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

4,799 views
4 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

4,686 views
4 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

3,173 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

3,137 views
3 citations

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

10,983 views
21 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

8,450 views
66 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

9,765 views
26 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

4,295 views
7 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

8,580 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

6,762 views
15 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

10,548 views
70 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

11,407 views
21 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

9,428 views
8 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

3,267 views
3 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

5,499 views
4 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

2,377 views

Original Research

Published on 19 Jan 2023

A Boolean-based machine learning framework identifies predictive biomarkers of HSP90-targeted therapy response in prostate cancer

in Biological Modeling and Simulation

Sung-Young Shin
Margaret M. Centenera
Joshua T. Hodgson
Elizabeth V. Nguyen
Lisa M. Butler
Roger J. Daly
Lan K. Nguyen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1094321

11,050 views
7 citations

Original Research

Published on 19 Jan 2023

Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer’s disease: An integrative molecular modeling approach

in Biological Modeling and Simulation

Rohit Shukla
Anuj Kumar
David J. Kelvin
Tiratha Raj Singh

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.1078987

7,439 views
17 citations

Original Research

Published on 16 Jan 2023

Small GTPase Ran: Depicting the nucleotide-specific conformational landscape of the functionally important C-terminus

in Biological Modeling and Simulation

Janka Czigleczki
Pedro Tulio de Resende Lara
Balint Dudas
Hyunbum Jang
David Perahia
Ruth Nussinov
Erika Balog

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2023.1111574

3,608 views
3 citations

Review

Published on 12 Jan 2023

Recent applications of computational methods to allosteric drug discovery

in Biological Modeling and Simulation

Rajiv Gandhi Govindaraj
Sundar Thangapandian
Michael Schauperl
Rajiah Aldrin Denny
David J. Diller

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.1070328

9,598 views
22 citations

494 articles

articles

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

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

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

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

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

Editorial: Biomolecular function and activity modulated by membranes

A Boolean-based machine learning framework identifies predictive biomarkers of HSP90-targeted therapy response in prostate cancer

Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer’s disease: An integrative molecular modeling approach

Small GTPase Ran: Depicting the nucleotide-specific conformational landscape of the functionally important C-terminus

Recent applications of computational methods to allosteric drug discovery