Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

3,035 views
12 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

2,027 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

4,981 views
7 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

2,967 views
4 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

4,419 views
10 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

2,281 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

970 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

4,278 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

2,645 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

2,302 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

1,760 views
1 citation

Technology and Code

Published on 15 Nov 2021

WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

in Biological Modeling and Simulation

Vincent Noël
Marco Ruscone
Gautier Stoll
Eric Viara
Andrei Zinovyev
Emmanuel Barillot
Laurence Calzone

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.754444

4,446 views
3 citations

Original Research

Published on 15 Nov 2021

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.2021.772486

4,221 views
9 citations

Editorial

Published on 12 Nov 2021

Editorial: Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics

in Biological Modeling and Simulation

Xiakun Chu
Yong Wang
Pengfei Tian
Wenfei Li
Davide Mercadante

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.795991

3,042 views
2 citations

Original Research

Published on 12 Nov 2021

Explore Protein Conformational Space With Variational Autoencoder

in Biological Modeling and Simulation

Hao Tian
Xi Jiang
Francesco Trozzi
Sian Xiao
Eric C. Larson
Peng Tao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.781635

11,079 views
38 citations

Original Research

Published on 08 Nov 2021

Prediction of Non-canonical Routes for SARS-CoV-2 Infection in Human Placenta Cells

in Biological Modeling and Simulation

Flávia Bessi Constantino
Sarah Santiloni Cury
Celia Regina Nogueira
Robson Francisco Carvalho
Luis Antonio Justulin

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.614728

4,197 views
18 citations