Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 26 Aug 2022

RL-MLZerD: Multimeric protein docking using reinforcement learning

in Biological Modeling and Simulation

Tunde Aderinwale
Charles Christoffer
Daisuke Kihara

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.969394

7,714 views
16 citations

Original Research

Published on 19 Aug 2022

A structural discovery journey of streptococcal phages adhesion devices by AlphaFold2

in Biological Modeling and Simulation

Adeline Goulet
Raphaela Joos
Katherine Lavelle
Douwe Van Sinderen
Jennifer Mahony
Christian Cambillau

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.960325

5,380 views
20 citations

Original Research

Published on 15 Aug 2022

The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation

in Biological Modeling and Simulation

Yaser Shabanpour
Sharareh Sajjadi
Esmaeil Behmard
Parviz Abdolmaleki
Amir Homayoun Keihan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.927373

3,762 views
7 citations

Original Research

Published on 15 Aug 2022

An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations

in Biological Modeling and Simulation

Adithya Polasa
Jeevapani Hettige
Kalyan Immadisetty
Mahmoud Moradi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.954262

3,893 views
8 citations

Original Research

Published on 15 Aug 2022

Predicting higher-order mutational effects in an RNA enzyme by machine learning of high-throughput experimental data

in Biological Modeling and Simulation

James D. Beck
Jessica M. Roberts
Joey M. Kitzhaber
Ashlyn Trapp
Edoardo Serra
Francesca Spezzano
Eric J. Hayden

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.893864

3,970 views
9 citations

Methods

Published on 12 Aug 2022

Improve the Colorectal Cancer Diagnosis Using Gut Microbiome Data

in Biological Modeling and Simulation

Yi-Hui Zhou
George Sun

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.921945

4,559 views
7 citations

Original Research

Published on 10 Aug 2022

A tumor microenvironment gene set–Based prognostic signature for non-small-cell lung cancer

in Biological Modeling and Simulation

Yingsheng Wen
Guangran Guo
Longjun Yang
Lianjuan Chen
Dechang Zhao
Xiaotian He
Rusi Zhang
Zirui Huang
Gongming Wang
Lanjun Zhang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.849108

4,978 views
4 citations

Mini Review

Published on 10 Aug 2022

Deep learning approaches for conformational flexibility and switching properties in protein design

in Biological Modeling and Simulation

Lucas S. P. Rudden
Mahdi Hijazi
Patrick Barth

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.928534

10,149 views
10 citations

Original Research

Published on 25 Jul 2022

MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field

in Biological Modeling and Simulation

Eman Alnabati
Juan Esquivel-Rodriguez
Genki Terashi
Daisuke Kihara

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.935411

5,393 views
8 citations

Brief Research Report

Published on 25 Jul 2022

Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics

in Biological Modeling and Simulation

Andrea Raffo
Luca Gagliardi
Ulderico Fugacci
Luca Sagresti
Simone Grandinetti
Giuseppe Brancato
Silvia Biasotti
Walter Rocchia

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.933924

4,201 views
2 citations

Original Research

Published on 22 Jul 2022

Decreased Interfacial Dynamics Caused by the N501Y Mutation in the SARS-CoV-2 S1 Spike:ACE2 Complex

in Biological Modeling and Simulation

Wesam S. Ahmed
Angelin M. Philip
Kabir H. Biswas

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.846996

4,885 views
19 citations

Mini Review

Published on 20 Jul 2022

Advances in UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Covalent Inhibition

in Biological Modeling and Simulation

Maycon Vinicius Damasceno de Oliveira
Renan Machado Furtado
Kauê S. da Costa
Serhii Vakal
Anderson H. Lima

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.889825

8,732 views
13 citations

Original Research

Published on 19 Jul 2022

Protein DEK and DTA Aptamers: Insight Into the Interaction Mechanisms and the Computational Aptamer Design

in Biological Modeling and Simulation

Lijun Dai
Jiangnan Zhang
Xiaonan Wang
Xiaoyue Yang
Feng Pan
Longhua Yang
Yongxing Zhao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.946480

4,433 views
3 citations

Original Research

Published on 19 Jul 2022

Effect of Cholesterol on C99 Dimerization: Revealed by Molecular Dynamics Simulations

in Biological Modeling and Simulation

Cheng-Dong Li
Muhammad Junaid
Xiaoqi Shan
Yanjing Wang
Xiangeng Wang
Abbas Khan
Dong-Qing Wei

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.872385

2,686 views
7 citations

Original Research

Published on 14 Jul 2022

Time-Optimal Adaptation in Metabolic Network Models

in Biological Modeling and Simulation

Markus A. Köbis
Alexander Bockmayr
Ralf Steuer

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.866676

2,874 views
5 citations

Brief Research Report

Published on 14 Jul 2022

Generalized Property-Based Encoders and Digital Signal Processing Facilitate Predictive Tasks in Protein Engineering

in Biological Modeling and Simulation

David Medina-Ortiz
Sebastian Contreras
Juan Amado-Hinojosa
Jorge Torres-Almonacid
Juan A. Asenjo
Marcelo Navarrete
Álvaro Olivera-Nappa

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.898627

3,644 views
15 citations

Original Research

Published on 12 Jul 2022

Mapping CAR T-Cell Design Space Using Agent-Based Models

in Biological Modeling and Simulation

Alexis N. Prybutok
Jessica S. Yu
Joshua N. Leonard
Neda Bagheri

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.849363

11,717 views
26 citations

Original Research

Published on 11 Jul 2022

Cations Do Not Alter the Membrane Structure of POPC—A Lipid With an Intermediate Area

in Biological Modeling and Simulation

Sergei Kurakin
Oleksandr Ivankov
Vadim Skoi
Alexander Kuklin
Daniela Uhríková
Norbert Kučerka

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.926591

5,862 views
8 citations

Original Research

Published on 08 Jul 2022

A Multi-Scale Approach to Model K+ Permeation Through the KcsA Channel

in Biological Modeling and Simulation

T. L. Horng
R. S. Chen
M. V. Leonardi
F. Franciolini
L. Catacuzzeno

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.880660

3,935 views
6 citations

Original Research

Published on 28 Jun 2022

Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations

in Biological Modeling and Simulation

Anil Ranu Mhashal
Ozge Yoluk
Laura Orellana

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2022.890851

4,900 views
4 citations

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

10,373 views
37 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

6,900 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

1,700 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

1,304 views

494 articles

articles

RL-MLZerD: Multimeric protein docking using reinforcement learning

A structural discovery journey of streptococcal phages adhesion devices by AlphaFold2

The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation

An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations

Predicting higher-order mutational effects in an RNA enzyme by machine learning of high-throughput experimental data

Improve the Colorectal Cancer Diagnosis Using Gut Microbiome Data

A tumor microenvironment gene set–Based prognostic signature for non-small-cell lung cancer

Deep learning approaches for conformational flexibility and switching properties in protein design

MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field

Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics

Decreased Interfacial Dynamics Caused by the N501Y Mutation in the SARS-CoV-2 S1 Spike:ACE2 Complex

Advances in UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Covalent Inhibition

Protein DEK and DTA Aptamers: Insight Into the Interaction Mechanisms and the Computational Aptamer Design

Effect of Cholesterol on C99 Dimerization: Revealed by Molecular Dynamics Simulations

Time-Optimal Adaptation in Metabolic Network Models

Generalized Property-Based Encoders and Digital Signal Processing Facilitate Predictive Tasks in Protein Engineering

Mapping CAR T-Cell Design Space Using Agent-Based Models

Cations Do Not Alter the Membrane Structure of POPC—A Lipid With an Intermediate Area

A Multi-Scale Approach to Model K+ Permeation Through the KcsA Channel

Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations

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