Original Research

Published on 28 Jun 2022

Evaluation of Clove Phytochemicals as Potential Antiviral Drug Candidates Targeting SARS-CoV-2 Main Protease: Computational Docking, Molecular Dynamics Simulation, and Pharmacokinetic Profiling

in Biological Modeling and Simulation

Arun Chandra Manivannan
Arunkumar Malaisamy
Murugesh Eswaran
Arun Meyyazhagan
Vijaya Anand Arumugam
Kannan R. R. Rengasamy
Balamuralikrishnan Balasubramanian
Wen-Chao Liu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.918101

6,110 views
21 citations

Original Research

Published on 27 Jun 2022

A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions

in Biological Modeling and Simulation

Shilpa Yadahalli
Lakshmi P. Jayanthi
Shachi Gosavi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.849272

5,070 views
1 citation

Editorial

Published on 22 Jun 2022

Editorial: Interaction of Biomolecules and Bioactive Compounds With the SARS-CoV-2 Proteins: Molecular Simulations for the Fight Against Covid-19

in Biological Modeling and Simulation

Mattia Falconi
James Leland Olds
Arvind Ramanathan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.950891

1,050 views

Correction

Published on 20 Jun 2022

Corrigendum: Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation

in Biological Modeling and Simulation

Yuan-Wei Ma
Tong-You Lin
Min-Yeh Tsai

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.944884

740 views

Original Research

Published on 13 Jun 2022

Collective Variable for Metadynamics Derived From AlphaFold Output

in Biological Modeling and Simulation

Vojtěch Spiwok
Martin Kurečka
Aleš Křenek

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.878133

7,574 views
12 citations

Original Research

Published on 02 Jun 2022

Hierarchical Virtual Screening Based on Rocaglamide Derivatives to Discover New Potential Anti-Skin Cancer Agents

in Biological Modeling and Simulation

Igor V.F. dos Santos
Rosivaldo S. Borges
Guilherme M. Silva
Lúcio R. de Lima
Ruan S. Bastos
Ryan S. Ramos
Luciane B. Silva
Carlos H. T. P. da Silva
Cleydson B. R. dos Santos

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.836572

3,053 views
11 citations

Original Research

Published on 01 Jun 2022

Validation of Deep Learning-Based DFCNN in Extremely Large-Scale Virtual Screening and Application in Trypsin I Protease Inhibitor Discovery

in Biological Modeling and Simulation

Haiping Zhang
Xiao Lin
Yanjie Wei
Huiling Zhang
Linbu Liao
Hao Wu
Yi Pan
Xuli Wu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.872086

1,968 views
6 citations

Original Research

Published on 31 May 2022

An Epistatic Network Describes oppA and glgB as Relevant Genes for Mycobacterium tuberculosis

in Biological Modeling and Simulation

Ali-Berenice Posada-Reyes
Yalbi I. Balderas-Martínez
Santiago Ávila-Ríos
Pablo Vinuesa
Salvador Fonseca-Coronado

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.856212

2,402 views
2 citations

Original Research

Published on 19 May 2022

Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach

in Biological Modeling and Simulation

Chuixiong Wu
Ruye Li
Kuang Yu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.851311

1,958 views
2 citations

Original Research

Published on 18 May 2022

Modeling Calcium Signaling in S. cerevisiae Highlights the Role and Regulation of the Calmodulin-Calcineurin Pathway in Response to Hypotonic Shock

in Biological Modeling and Simulation

Simone Spolaor
Mattia Rovetta
Marco S. Nobile
Paolo Cazzaniga
Renata Tisi
Daniela Besozzi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.856030

3,174 views
3 citations

Original Research

Published on 16 May 2022

Predicting Metabolic Adaptation Under Dynamic Substrate Conditions Using a Resource-Dependent Kinetic Model: A Case Study Using Saccharomyces cerevisiae

in Biological Modeling and Simulation

K. J. A. Verhagen
S. A. Eerden
B. J. Sikkema
S. A. Wahl

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.863470

2,182 views
1 citation

Original Research

Published on 10 May 2022

Potential of Natural Alkaloids From Jadwar (Delphinium denudatum) as Inhibitors Against Main Protease of COVID-19: A Molecular Modeling Approach

in Biological Modeling and Simulation

Anuj Kumar
Mansi Sharma
Christopher D. Richardson
David J. Kelvin

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.898874

3,984 views
5 citations

Original Research

Published on 04 May 2022

Discrete Biochemical Systems Theory

in Biological Modeling and Simulation

Eberhard O. Voit
Daniel V. Olivença

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.874669

2,739 views
5 citations

Original Research

Published on 02 May 2022

Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations

in Biological Modeling and Simulation

Rajarshi Roy
Nisha Amarnath Jonniya
Md Fulbabu Sk
Parimal Kar

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.852895

2,381 views
5 citations

Review

Published on 29 Apr 2022

Generalized Structural Kinetic Modeling: A Survey and Guide

in Biological Modeling and Simulation

Jana C. Massing
Thilo Gross

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.825052

1,938 views

Original Research

Published on 28 Apr 2022

Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis

in Biological Modeling and Simulation

Khyber Shinwari
Hafiz Muzzammel Rehman
Guojun Liu
Mikhail A. Bolkov
Irina A. Tuzankina
Valery. A. Chereshnev

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.879875

4,978 views
15 citations

Navigation group

Articles

Evaluation of Clove Phytochemicals as Potential Antiviral Drug Candidates Targeting SARS-CoV-2 Main Protease: Computational Docking, Molecular Dynamics Simulation, and Pharmacokinetic Profiling

A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions

Editorial: Interaction of Biomolecules and Bioactive Compounds With the SARS-CoV-2 Proteins: Molecular Simulations for the Fight Against Covid-19

Corrigendum: Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation

Collective Variable for Metadynamics Derived From AlphaFold Output

Hierarchical Virtual Screening Based on Rocaglamide Derivatives to Discover New Potential Anti-Skin Cancer Agents

Validation of Deep Learning-Based DFCNN in Extremely Large-Scale Virtual Screening and Application in Trypsin I Protease Inhibitor Discovery

An Epistatic Network Describes oppA and glgB as Relevant Genes for Mycobacterium tuberculosis

Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach

Modeling Calcium Signaling in S. cerevisiae Highlights the Role and Regulation of the Calmodulin-Calcineurin Pathway in Response to Hypotonic Shock

Predicting Metabolic Adaptation Under Dynamic Substrate Conditions Using a Resource-Dependent Kinetic Model: A Case Study Using Saccharomyces cerevisiae

Potential of Natural Alkaloids From Jadwar (Delphinium denudatum) as Inhibitors Against Main Protease of COVID-19: A Molecular Modeling Approach

Discrete Biochemical Systems Theory

Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations

Generalized Structural Kinetic Modeling: A Survey and Guide

Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis