Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 24 Jan 2022

A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease

in Biological Modeling and Simulation

Jorge E. Hernández González
Raphael J. Eberle
Dieter Willbold
Mônika A. Coronado

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.816166

5,229 views
11 citations

Original Research

Published on 24 Jan 2022

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

in Biological Modeling and Simulation

Vivek S. Bharadwaj
Luke P. Westawker
Michael F. Crowley

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.756219

2,963 views

Editorial

Published on 24 Jan 2022

Editorial: Coarse-Grained Models of Nucleic Acids and Their Applications

in Biological Modeling and Simulation

Maciej Maciejczyk

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.842049

1,967 views

Original Research

Published on 21 Jan 2022

Prediction of Residue-specific Contributions to Binding and Thermal Stability Using Yeast Surface Display

in Biological Modeling and Simulation

Shahbaz Ahmed
Munmun Bhasin
Kavyashree Manjunath
Raghavan Varadarajan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.800819

6,938 views
31 citations

Review

Published on 14 Jan 2022

From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus

in Biological Modeling and Simulation

Elnaz Aledavood
Beatrice Selmi
Carolina Estarellas
Matteo Masetti
F. Javier Luque

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.796229

6,300 views
13 citations

Methods

Published on 05 Jan 2022

QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure

in Biological Modeling and Simulation

Sucharita Dey
Jaime Prilusky
Emmanuel D. Levy

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.787510

5,308 views
8 citations

Original Research

Published on 03 Jan 2022

2-Sulfonylpyrimidines as Privileged Warheads for the Development of S. aureus Sortase A Inhibitors

in Biological Modeling and Simulation

Fabian Barthels
Jessica Meyr
Stefan J. Hammerschmidt
Tessa Marciniak
Hans-Joachim Räder
Wilma Ziebuhr
Bernd Engels
Tanja Schirmeister

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.804970

5,599 views
12 citations

Original Research

Published on 23 Dec 2021

Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins

in Biological Modeling and Simulation

Yann Chalopin
Julien Sparfel

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.736376

2,612 views
9 citations

Review

Published on 22 Dec 2021

Membrane-Mediated Interactions Between Protein Inclusions

in Biological Modeling and Simulation

Jie Gao
Ruihan Hou
Long Li
Jinglei Hu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.811711

6,104 views
13 citations

Original Research

Published on 20 Dec 2021

A Novel Hybrid Logic-ODE Modeling Approach to Overcome Knowledge Gaps

in Biological Modeling and Simulation

Gianluca Selvaggio
Serena Cristellon
Luca Marchetti

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.760077

4,118 views
6 citations

Original Research

Published on 20 Dec 2021

Exploring Kv1.2 Channel Inactivation Through MD Simulations and Network Analysis

in Biological Modeling and Simulation

Flavio Costa
Carlo Guardiani
Alberto Giacomello

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.784276

4,132 views
9 citations

Technology and Code

Published on 17 Dec 2021

Understanding Metabolic Flux Behaviour in Whole-Cell Model Output

in Biological Modeling and Simulation

Sophie Landon
Oliver Chalkley
Gus Breese
Claire Grierson
Lucia Marucci

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.732079

4,328 views
8 citations

Original Research

Published on 14 Dec 2021

Unveiling the Gating Mechanism of CRAC Channel: A Computational Study

in Biological Modeling and Simulation

Carlo Guardiani
Delia Sun
Alberto Giacomello

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.773388

6,063 views
11 citations

Original Research

Published on 14 Dec 2021

RIGI, TLR7, and TLR3 Genes Were Predicted to Have Immune Response Against Avian Influenza in Indigenous Ducks

in Biological Modeling and Simulation

Aruna Pal
Abantika Pal
Pradyumna Baviskar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.633283

4,124 views
16 citations

Original Research

Published on 13 Dec 2021

Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin

in Biological Modeling and Simulation

Zhiyuan Qu
Kaihang Li
Xiaoju Geng
Bo Huang
Jian Gao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.791885

2,700 views
6 citations

Original Research

Published on 13 Dec 2021

Identification and Validation of ATF3 Serving as a Potential Biomarker and Correlating With Pharmacotherapy Response and Immune Infiltration Characteristics in Rheumatoid Arthritis

in Biological Modeling and Simulation

Huan Hu
Facai Zhang
Li Li
Jun Liu
Qin Ao
Ping Li
Jiashun Zeng
Long Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.761841

6,099 views
10 citations

Editorial

Published on 09 Dec 2021

Editorial: Computational Approaches to Study the Impact of Mutations on Disease and Drug Resistance

in Biological Modeling and Simulation

Nir Ben-Tal
Daisuke Kihara
Arun Prasad Pandurangan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.813552

3,753 views
5 citations

Original Research

Published on 09 Dec 2021

Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2

in Biological Modeling and Simulation

Adebiyi Sobitan
Vidhyanand Mahase
Raina Rhoades
Dejaun Williams
Dongxiao Liu
Yixin Xie
Lin Li
Qiyi Tang
Shaolei Teng

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.784303

5,361 views
12 citations

Hypothesis and Theory

Published on 07 Dec 2021

A Mathematical Model to Characterize the Role of Light Adaptation in Mammalian Circadian Clock

in Biological Modeling and Simulation

Yuzeng Shi
Yu Liu
Ling Yang
Jie Yan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.681696

3,077 views
1 citation

Correction

Published on 07 Dec 2021

Corrigendum: Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models

in Biological Modeling and Simulation

Genki Shino
Shoji Takada

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.817343

1,388 views
1 citation

Brief Research Report

Published on 06 Dec 2021

PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound–Protein Interactions

in Biological Modeling and Simulation

Kazuyoshi Ikeda
Takuo Doi
Masami Ikeda
Kentaro Tomii

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.758480

5,266 views
1 citation

Editorial

Published on 03 Dec 2021

Editorial: Machine Learning Methodologies to Study Molecular Interactions

in Biological Modeling and Simulation

Artur Yakimovich
Arzucan Özgür
Tunca Doğan
Elif Ozkirimli

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.806474

3,139 views
1 citation

Editorial

Published on 29 Nov 2021

Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function

in Biological Modeling and Simulation

Maya Topf
Edina Rosta
Gregory R. Bowman
Massimiliano Bonomi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.799406

2,863 views

Editorial

Published on 19 Nov 2021

Editorial: Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events

in Biological Modeling and Simulation

Fabio Trovato
Joanna Trylska
Peter J. Bond
Peter G. Wolynes

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.797754

2,364 views
2 citations

494 articles

articles

A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Editorial: Coarse-Grained Models of Nucleic Acids and Their Applications

Prediction of Residue-specific Contributions to Binding and Thermal Stability Using Yeast Surface Display

From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus

QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure

2-Sulfonylpyrimidines as Privileged Warheads for the Development of S. aureus Sortase A Inhibitors

Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins

Membrane-Mediated Interactions Between Protein Inclusions

A Novel Hybrid Logic-ODE Modeling Approach to Overcome Knowledge Gaps

Exploring Kv1.2 Channel Inactivation Through MD Simulations and Network Analysis

Understanding Metabolic Flux Behaviour in Whole-Cell Model Output

Unveiling the Gating Mechanism of CRAC Channel: A Computational Study

RIGI, TLR7, and TLR3 Genes Were Predicted to Have Immune Response Against Avian Influenza in Indigenous Ducks

Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin

Identification and Validation of ATF3 Serving as a Potential Biomarker and Correlating With Pharmacotherapy Response and Immune Infiltration Characteristics in Rheumatoid Arthritis

Editorial: Computational Approaches to Study the Impact of Mutations on Disease and Drug Resistance

Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2

A Mathematical Model to Characterize the Role of Light Adaptation in Mammalian Circadian Clock

Corrigendum: Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models

PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound–Protein Interactions

Editorial: Machine Learning Methodologies to Study Molecular Interactions

Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function

Editorial: Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events