Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 29 Jun 2021

Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein–Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis

in Biological Modeling and Simulation

Huma Farooque Hashmi
Muhammad Waseem
Syed Shujait Ali
Zahid Hussain
Kaoshan Chen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.664436

3,199 views

Original Research

Published on 28 Jun 2021

Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs

in Biological Modeling and Simulation

Matteo Lambrughi
Emiliano Maiani
Burcu Aykac Fas
Gary S. Shaw
Birthe B. Kragelund
Kresten Lindorff-Larsen
Kaare Teilum
Gaetano Invernizzi
Elena Papaleo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.676235

9,738 views
14 citations

Mini Review

Published on 28 Jun 2021

Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data

in Biological Modeling and Simulation

Vandana Yadav
Inayat Ullah Irshad
Hemant Kumar
Ajeet K. Sharma

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.688700

10,311 views
14 citations

Original Research

Published on 23 Jun 2021

Elucidating Axonal Injuries Through Molecular Modelling of Myelin Sheaths and Nodes of Ranvier

in Biological Modeling and Simulation

Marzieh Saeedimasine
Annaclaudia Montanino
Svein Kleiven
Alessandra Villa

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.669897

3,640 views
13 citations

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

3,756 views
3 citations

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

26,636 views
62 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

5,030 views
8 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

12,815 views
27 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

3,180 views
9 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

23,897 views
43 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

3,737 views
10 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

7,533 views
44 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

3,851 views
14 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

3,944 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

6,523 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

1,708 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

7,493 views
13 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

21,026 views
104 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

5,788 views
3 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

3,781 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

4,573 views
13 citations

Original Research

Published on 19 May 2021

HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes

in Biological Modeling and Simulation

Mohamad Harastani
Mikhail Eltsov
Amélie Leforestier
Slavica Jonic

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.663121

6,486 views
47 citations

Original Research

Published on 18 May 2021

Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach

in Biological Modeling and Simulation

Mateusz Olek
Agnel Praveen Joseph

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.652530

5,101 views
7 citations

Original Research

Published on 17 May 2021

Ranking-Based Convolutional Neural Network Models for Peptide-MHC Class I Binding Prediction

in Biological Modeling and Simulation

Ziqi Chen
Martin Renqiang Min
Xia Ning

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.634836

6,245 views
14 citations

494 articles

articles

Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein–Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis

Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs

Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data

Elucidating Axonal Injuries Through Molecular Modelling of Myelin Sheaths and Nodes of Ranvier

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

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

Thermodynamic Origin of Differential Excipient-Lysozyme Interactions

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

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

HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes

Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach

Ranking-Based Convolutional Neural Network Models for Peptide-MHC Class I Binding Prediction