Original Research

Published on 29 Apr 2021

A Deep Graph Network–Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins

in Biological Modeling and Simulation

Federico Errica
Marco Giulini
Davide Bacciu
Roberto Menichetti
Alessio Micheli
Raffaello Potestio

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.637396

4,043 views
12 citations

Brief Research Report

Published on 27 Apr 2021

Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor

in Biological Modeling and Simulation

Hung N. Do
Sana Akhter
Yinglong Miao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.673170

13,848 views
14 citations

Original Research

Published on 22 Apr 2021

The Effect of Cholesterol on Membrane-Bound Islet Amyloid Polypeptide

in Biological Modeling and Simulation

Mikkel Christensen
Nils A. Berglund
Birgit Schiøtt

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.657946

3,101 views
8 citations

Original Research

Published on 22 Apr 2021

MD Simulations on a Well-Built Docking Model Reveal Fine Mechanical Stability and Force-Dependent Dissociation of Mac-1/GPIbα Complex

in Biological Modeling and Simulation

Xiaoyan Jiang
Xiaoxi Sun
Jiangguo Lin
Yingchen Ling
Ying Fang
Jianhua Wu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.638396

3,013 views
6 citations

Original Research

Published on 22 Apr 2021

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods

in Biological Modeling and Simulation

Mustapha Carab Ahmed
Line K. Skaanning
Alexander Jussupow
Estella A. Newcombe
Birthe B. Kragelund
Carlo Camilloni
Annette E. Langkilde
Kresten Lindorff-Larsen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.654333

6,767 views
66 citations

Editorial

Published on 21 Apr 2021

Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design

in Biological Modeling and Simulation

Guang Hu
Pemra Doruker
Hongchun Li
Ebru Demet Akten

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.681364

3,128 views
5 citations

Original Research

Published on 20 Apr 2021

Shark Antibody Variable Domains Rigidify Upon Affinity Maturation—Understanding the Potential of Shark Immunoglobulins as Therapeutics

in Biological Modeling and Simulation

Monica L. Fernández-Quintero
Clarissa A. Seidler
Patrick K. Quoika
Klaus R. Liedl

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.639166

7,038 views
9 citations

Original Research

Published on 19 Apr 2021

Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks

in Biological Modeling and Simulation

Elena Díaz-Santiago
M. Gonzalo Claros
Raquel Yahyaoui
Yolanda de Diego-Otero
Rocío Calvo
Janet Hoenicka
Francesc Palau
Juan A. G. Ranea
James R. Perkins

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.635074

4,137 views
4 citations

Perspective

Published on 15 Apr 2021

Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist’s Perspective

in Biological Modeling and Simulation

Fotis L. Kyrilis
Jaydeep Belapure
Panagiotis L. Kastritis

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.660542

4,217 views
12 citations

Original Research

Published on 15 Apr 2021

Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins

in Biological Modeling and Simulation

Chengtao Ding
Sheng Wang
Zhiyong Zhang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.621128

2,094 views
5 citations

Original Research

Published on 13 Apr 2021

Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

in Biological Modeling and Simulation

Chenjie Feng
Ya-Lan Tan
Yu-Xuan Cheng
Ya-Zhou Shi
Zhi-Jie Tan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.666369

2,923 views
13 citations

Editorial

Published on 13 Apr 2021

Editorial: Molecular Dynamics and Machine Learning in Drug Discovery

in Biological Modeling and Simulation

Sergio Decherchi
Francesca Grisoni
Pratyush Tiwary
Andrea Cavalli

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.673773

4,494 views
8 citations

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

3,682 views
14 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

3,422 views
6 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

4,936 views
21 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

8,016 views
23 citations

Navigation group

Articles

A Deep Graph Network–Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins

Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor

The Effect of Cholesterol on Membrane-Bound Islet Amyloid Polypeptide

MD Simulations on a Well-Built Docking Model Reveal Fine Mechanical Stability and Force-Dependent Dissociation of Mac-1/GPIbα Complex

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods

Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design

Shark Antibody Variable Domains Rigidify Upon Affinity Maturation—Understanding the Potential of Shark Immunoglobulins as Therapeutics

Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks

Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist’s Perspective

Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins

Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

Editorial: Molecular Dynamics and Machine Learning in Drug Discovery

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

Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model

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

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