Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Original Research

Published on 17 May 2021

An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

in Biological Modeling and Simulation

Tianhua Zhai
Fangyuan Zhang
Shozeb Haider
Daniel Kraut
Zuyi Huang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.661424

6,842 views
21 citations

Review

Published on 11 May 2021

Reconciling Simulations and Experiments With BICePs: A Review

in Biological Modeling and Simulation

Vincent A. Voelz
Yunhui Ge
Robert M. Raddi

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.661520

3,565 views
16 citations

Original Research

Published on 10 May 2021

Molecular Mechanics Study of Flow and Surface Influence in Ligand–Protein Association

in Biological Modeling and Simulation

Shivansh Kaushik
Chia-en A. Chang

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.659687

3,291 views
4 citations

Original Research

Published on 07 May 2021

Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach

in Biological Modeling and Simulation

Alessandra de Felice
Simone Aureli
Vittorio Limongelli

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.673053

8,681 views
12 citations

Original Research

Published on 07 May 2021

ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor

in Biological Modeling and Simulation

Onur Can Karabulut
Betül Asiye Karpuzcu
Erdem Türk
Ahmad Hassan Ibrahim
Barış Ethem Süzek

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.647424

5,105 views
16 citations

Review

Published on 07 May 2021

Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae

in Biological Modeling and Simulation

Sundeep Chaitanya Vedithi
Sony Malhotra
Marta Acebrón-García-de-Eulate
Modestas Matusevicius
Pedro Henrique Monteiro Torres
Tom L. Blundell

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.663301

5,827 views
3 citations

Original Research

Published on 07 May 2021

Mapping OMIM Disease–Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes

in Biological Modeling and Simulation

Castrense Savojardo
Giulia Babbi
Pier Luigi Martelli
Rita Casadio

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.617016

4,743 views
10 citations

Review

Published on 05 May 2021

Artificial Intelligence in Epigenetic Studies: Shedding Light on Rare Diseases

in Biological Modeling and Simulation

Sandra Brasil
Cátia José Neves
Tatiana Rijoff
Marta Falcão
Gonçalo Valadão
Paula A. Videira
Vanessa dos Reis Ferreira

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.648012

15,292 views
39 citations

Original Research

Published on 04 May 2021

DESP: Deep Enhanced Sampling of Proteins’ Conformation Spaces Using AI-Inspired Biasing Forces

in Biological Modeling and Simulation

Emmanuel Oluwatobi Salawu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.587151

5,131 views
8 citations

Original Research

Published on 03 May 2021

Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation

in Biological Modeling and Simulation

Sohini Chakraborti
Moubani Chakraborty
Avipsa Bose
Narayanaswamy Srinivasan
Sandhya S. Visweswariah

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.599221

9,585 views
17 citations

Original Research

Published on 30 Apr 2021

A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism

in Biological Modeling and Simulation

Alessandro Crnjar
Susanne M. Mesoy
Sarah C. R. Lummis
Carla Molteni

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.644720

3,955 views
5 citations

Original Research

Published on 30 Apr 2021

Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2

in Biological Modeling and Simulation

Jacopo Sgrignani
Andrea Cavalli

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.666626

8,896 views
8 citations

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

5,517 views
17 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

20,492 views
23 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

4,255 views
10 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

9,306 views
89 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

4,284 views
7 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

5,374 views
10 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

9,212 views
12 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

5,576 views
6 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

5,482 views
14 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

3,068 views
5 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

5,907 views
9 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

4,210 views
15 citations

494 articles

articles

An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

Reconciling Simulations and Experiments With BICePs: A Review

Molecular Mechanics Study of Flow and Surface Influence in Ligand–Protein Association

Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach

ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor

Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae

Mapping OMIM Disease–Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes

Artificial Intelligence in Epigenetic Studies: Shedding Light on Rare Diseases

DESP: Deep Enhanced Sampling of Proteins’ Conformation Spaces Using AI-Inspired Biasing Forces

Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation

A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism

Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2

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

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

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

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

Editorial: Molecular Dynamics and Machine Learning in Drug Discovery

Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement