Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Review

Published on 17 Jun 2021

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

in Biological Modeling and Simulation

A. Sengar
T. E. Ouldridge
O. Henrich
L. Rovigatti
P. Šulc

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.693710

21,982 views
51 citations

Original Research

Published on 14 Jun 2021

Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl

in Biological Modeling and Simulation

Tülay Karakulak
Ahmet Sureyya Rifaioglu
João P. G. L. M. Rodrigues
Ezgi Karaca

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.658906

4,111 views
7 citations

Original Research

Published on 11 Jun 2021

N6-Methyladenosine RNA Methylation Regulator-Related Alternative Splicing (AS) Gene Signature Predicts Non–Small Cell Lung Cancer Prognosis

in Biological Modeling and Simulation

Zhenyu Zhao
Qidong Cai
Pengfei Zhang
Boxue He
Xiong Peng
Guangxu Tu
Weilin Peng
Li Wang
Fenglei Yu
Xiang Wang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.657087

11,584 views
25 citations

Original Research

Published on 11 Jun 2021

Thermodynamic Origin of Differential Excipient-Lysozyme Interactions

in Biological Modeling and Simulation

Jas Kalayan
Robin A. Curtis
Jim Warwicker
Richard H. Henchman

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.689400

2,415 views
8 citations

Review

Published on 10 Jun 2021

Learning the Regulatory Code of Gene Expression

in Biological Modeling and Simulation

Jan Zrimec
Filip Buric
Mariia Kokina
Victor Garcia
Aleksej Zelezniak

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.673363

20,752 views
29 citations

Review

Published on 07 Jun 2021

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

in Biological Modeling and Simulation

Marco Giulini
Marta Rigoli
Giovanni Mattiotti
Roberto Menichetti
Thomas Tarenzi
Raffaele Fiorentini
Raffaello Potestio

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.676976

6,335 views
37 citations

Original Research

Published on 07 Jun 2021

Structural Basis of the Function of Yariv Reagent—An Important Tool to Study Arabinogalactan Proteins

in Biological Modeling and Simulation

Tereza Přerovská
Anna Pavlů
Dzianis Hancharyk
Anna Rodionova
Anna Vavříková
Vojtěch Spiwok

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.682858

2,967 views
9 citations

Original Research

Published on 07 Jun 2021

Nascent Folding of Proteins Across the Three Domains of Life

in Biological Modeling and Simulation

Mateusz Chwastyk
Marek Cieplak

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.692230

3,101 views
12 citations

Original Research

Published on 04 Jun 2021

Automatic Bayesian Weighting for SAXS Data

in Biological Modeling and Simulation

Yannick G. Spill
Yasaman Karami
Pierre Maisonneuve
Nicolas Wolff
Michael Nilges

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.671011

3,040 views
5 citations

Original Research

Published on 02 Jun 2021

Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer’s Disease on the Orthosteric Site

in Biological Modeling and Simulation

Alejandro Soto-Ospina
Pedronel Araque Marín
Gabriel Bedoya
Diego Sepulveda-Falla
Andrés Villegas Lanau

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.649990

5,458 views
6 citations

Correction

Published on 28 May 2021

Corrigendum: Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

in Biological Modeling and Simulation

Łukasz Nierzwicki
Giulia Palermo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.698735

1,364 views

Original Research

Published on 26 May 2021

How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case

in Biological Modeling and Simulation

Cristina Paissoni
Carlo Camilloni

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.694130

6,125 views
10 citations

Original Research

Published on 25 May 2021

Protein Docking Model Evaluation by Graph Neural Networks

in Biological Modeling and Simulation

Xiao Wang
Sean T. Flannery
Daisuke Kihara

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.647915

17,841 views
91 citations

Original Research

Published on 24 May 2021

Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction

in Biological Modeling and Simulation

Ennys Gheyouche
Matthias Bagueneau
Gervaise Loirand
Bernard Offmann
Stéphane Téletchéa

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.643728

4,870 views
2 citations

Original Research

Published on 21 May 2021

Bayesian Random Tomography of Particle Systems

in Biological Modeling and Simulation

Nima Vakili
Michael Habeck

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.658269

3,185 views
2 citations

Original Research

Published on 20 May 2021

Insights Into Mutations Induced Conformational Changes and Rearrangement of Fe2+ Ion in pncA Gene of Mycobacterium tuberculosis to Decipher the Mechanism of Resistance to Pyrazinamide

in Biological Modeling and Simulation

Asma Sindhoo Nangraj
Abbas Khan
Shaheena Umbreen
Sana Sahar
Maryam Arshad
Saba Younas
Sajjad Ahmad
Shahid Ali
Syed Shujait Ali
Liaqat Ali

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.633365

3,699 views
9 citations