Original Research

Published on 17 Jun 2021

BowSaw: Inferring Higher-Order Trait Interactions Associated With Complex Biological Phenotypes

in Biological Modeling and Simulation

Demetrius DiMucci
Mark Kon
Daniel Segrè

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.663532

2,661 views
1 citation

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

19,320 views
47 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

3,763 views
7 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

2,131 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

10,976 views
20 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

18,947 views
25 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

2,623 views
9 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

5,744 views
34 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

2,813 views
9 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

2,754 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

5,038 views
5 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

1,239 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

5,593 views
7 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

16,322 views
73 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

4,333 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

2,894 views
2 citations

Navigation group

Articles

BowSaw: Inferring Higher-Order Trait Interactions Associated With Complex Biological Phenotypes

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

Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl

Thermodynamic Origin of Differential Excipient-Lysozyme Interactions

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

Learning the Regulatory Code of Gene Expression

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

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

Nascent Folding of Proteins Across the Three Domains of Life

Automatic Bayesian Weighting for SAXS Data

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

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

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

Protein Docking Model Evaluation by Graph Neural Networks

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

Bayesian Random Tomography of Particle Systems