Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 12 Apr 2021

Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions

in Biological Modeling and Simulation

Irina Ritsch
Laura Esteban-Hofer
Elisabeth Lehmann
Leonidas Emmanouilidis
Maxim Yulikov
Frédéric H.-T. Allain
Gunnar Jeschke

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.636599

4,897 views
16 citations

Original Research

Published on 12 Apr 2021

Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model

in Biological Modeling and Simulation

Chengwei Zhang
Jing Huang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.624679

4,961 views
9 citations

Original Research

Published on 09 Apr 2021

Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2

in Biological Modeling and Simulation

Thirumal Kumar D
Nishaat Shaikh
Udhaya Kumar S
George Priya Doss C
Hatem Zayed

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.645216

6,261 views
25 citations

Opinion

Published on 05 Apr 2021

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.2021.641208

10,303 views
28 citations

Original Research

Published on 01 Apr 2021

Delayed Modeling Approach to Forecast the Periodic Behavior of SARS-2

in Biological Modeling and Simulation

Zhenhua Yu
Ayesha Sohail
Alessandro Nutini
Robia Arif

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2020.585245

3,879 views
25 citations

Original Research

Published on 30 Mar 2021

Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders

in Biological Modeling and Simulation

Rodrigo Ochoa
Roman A. Laskowski
Janet M. Thornton
Pilar Cossio

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.636562

3,556 views
5 citations

Perspective

Published on 29 Mar 2021

Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

in Biological Modeling and Simulation

Paulo C. T. Souza
Vittorio Limongelli
Sangwook Wu
Siewert J. Marrink
Luca Monticelli

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.657222

12,893 views
39 citations

Methods

Published on 25 Mar 2021

ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed

in Biological Modeling and Simulation

Paola Turina
Piero Fariselli
Emidio Capriotti

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.620475

4,074 views
7 citations

Brief Research Report

Published on 25 Mar 2021

Molecular Basis of Class B GPCR Selectivity for the Neuropeptides PACAP and VIP

in Biological Modeling and Simulation

Chenyi Liao
Jacob M. Remington
Victor May
Jianing Li

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.644644

5,995 views
25 citations

Original Research

Published on 19 Mar 2021

Insight Into Seeded Tau Fibril Growth From Molecular Dynamics Simulation of the Alzheimer’s Disease Protofibril Core

in Biological Modeling and Simulation

Cass Leonard
Christian Phillips
James McCarty

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.624302

8,590 views
29 citations

Original Research

Published on 19 Mar 2021

Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution

in Biological Modeling and Simulation

Marta Kulik
Takaharu Mori
Yuji Sugita

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.631854

7,758 views
17 citations

Original Research

Published on 18 Mar 2021

Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants

in Biological Modeling and Simulation

Yannick Mahlich
Maximillian Miller
Zishuo Zeng
Yana Bromberg

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.635382

2,998 views
3 citations

Review

Published on 17 Mar 2021

Bottom-Up Coarse-Grained Modeling of DNA

in Biological Modeling and Simulation

Tiedong Sun
Vishal Minhas
Nikolay Korolev
Alexander Mirzoev
Alexander P. Lyubartsev
Lars Nordenskiöld

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.645527

9,100 views
45 citations

Original Research

Published on 16 Mar 2021

Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition

in Biological Modeling and Simulation

Yogesh B. Narkhede
Avneesh K. Gautam
Rohaine V. Hsu
Wilson Rodriguez
Nehemiah T. Zewde
Reed E. S. Harrison
Pablo R. Arantes
Zied Gaieb
Ronald D. Gorham
Chris Kieslich

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.618068

3,858 views
1 citation

Original Research

Published on 12 Mar 2021

Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands

in Biological Modeling and Simulation

Guangfeng Shao
Jingxiao Bao
Xiaolin Pan
Xiao He
Yifei Qi
John Z. H. Zhang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.646524

5,498 views
9 citations

Original Research

Published on 11 Mar 2021

Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets

in Biological Modeling and Simulation

Munmun Bhasin
Raghavan Varadarajan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.635425

7,359 views
19 citations

Brief Research Report

Published on 11 Mar 2021

CUTie2: The Attack of the Cyclic Nucleotide Sensor Clones

in Biological Modeling and Simulation

Florencia Klein
Florencia Sardi
Matías R. Machado
Claudia Ortega
Marcelo A. Comini
Sergio Pantano

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.629773

4,347 views
6 citations

Brief Research Report

Published on 10 Mar 2021

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

in Biological Modeling and Simulation

Sotaro Fuchigami
Toru Niina
Shoji Takada

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.636940

2,855 views
13 citations

Original Research

Published on 10 Mar 2021

Influence of Disease-Causing Mutations on Protein Structural Networks

in Biological Modeling and Simulation

Vasam Manjveekar Prabantu
Nagarajan Naveenkumar
Narayanaswamy Srinivasan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2020.620554

48,521 views
63 citations

Original Research

Published on 04 Mar 2021

The Morphology of Hydroxyapatite Nanoparticles Regulates Cargo Recognition in Clathrin-Mediated Endocytosis

in Biological Modeling and Simulation

Cheng Zhu
Xuejie Zhou
Ziteng Liu
Hongwei Chen
Hongfeng Wu
Xiao Yang
Xiangdong Zhu
Jing Ma
Hao Dong

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.627015

5,808 views
22 citations

Original Research

Published on 23 Feb 2021

Albumin Alters the Conformational Ensemble of Amyloid-β by Promiscuous Interactions: Implications for Amyloid Inhibition

in Biological Modeling and Simulation

Huisi Xie
Cong Guo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2020.629520

5,601 views
30 citations

Original Research

Published on 22 Feb 2021

Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane

in Biological Modeling and Simulation

Md. Iqbal Mahmood
Adolfo B. Poma
Kei-ichi Okazaki

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.619381

14,670 views
46 citations

Original Research

Published on 18 Feb 2021

Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection

in Biological Modeling and Simulation

Piotr Chyży
Marta Kulik
Suyong Re
Yuji Sugita
Joanna Trylska

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.633130

7,951 views
16 citations

Original Research

Published on 15 Feb 2021

Molecular Mechanisms Behind Anti SARS-CoV-2 Action of Lactoferrin

in Biological Modeling and Simulation

Mattia Miotto
Lorenzo Di Rienzo
Leonardo Bò
Alberto Boffi
Giancarlo Ruocco
Edoardo Milanetti

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.607443

7,978 views
50 citations