Frontiers in Molecular Biosciences | Biological Modeling and Simulation

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

5,561 views
41 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

3,991 views
5 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

4,876 views
12 citations

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

5,481 views
19 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

2,543 views
12 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

2,556 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

6,483 views
7 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

4,121 views
14 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

4,577 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

3,585 views
7 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

13,120 views
27 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

4,251 views
6 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

8,566 views
14 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

3,186 views
4 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

7,541 views
6 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

4,382 views
13 citations