Original Research

Published on 09 Jul 2019

Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase

in Biological Modeling and Simulation

Feng Wang
Li Shen
Hongyu Zhou
Shouyi Wang
Xinlei Wang
Peng Tao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00047

4,829 views
18 citations

Opinion

Published on 02 Jul 2019

Building Minimalist Models for Functionalized Metal Nanoparticles

in Biological Modeling and Simulation

Giorgia Brancolini
Valentina Tozzini

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00050

2,913 views
6 citations

Original Research

Published on 19 Jun 2019

Using Dimensionality Reduction to Analyze Protein Trajectories

in Biological Modeling and Simulation

Gareth A. Tribello
Piero Gasparotto

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00046

13,269 views
61 citations

Original Research

Published on 12 Jun 2019

Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods

in Biological Modeling and Simulation

Gianmarc Grazioli
Rachel W. Martin
Carter T. Butts

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00042

5,896 views
26 citations

Original Research

Published on 11 Jun 2019

Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations

in Biological Modeling and Simulation

Steve Agajanian
Odeyemi Oluyemi
Gennady M. Verkhivker

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00044

18,204 views
45 citations

Original Research

Published on 24 May 2019

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

in Biological Modeling and Simulation

Daria B. Kokh
Tom Kaufmann
Bastian Kister
Rebecca C. Wade

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00036

8,970 views
45 citations

Review

Published on 03 May 2019

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations

in Biological Modeling and Simulation

Mercedes Alfonso-Prieto
Luciano Navarini
Paolo Carloni

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00029

19,968 views
29 citations

Original Research

Published on 18 Apr 2019

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations

in Biological Modeling and Simulation

Dalibor Trapl
Izabela Horvacanin
Vaclav Mareska
Furkan Ozcelik
Gozde Unal
Vojtech Spiwok

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00025

9,262 views
28 citations

Original Research

Published on 18 Apr 2019

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

in Biological Modeling and Simulation

Benjamin A. Helfrecht
Piero Gasparotto
Federico Giberti
Michele Ceriotti

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00024

3,653 views
10 citations

Original Research

Published on 10 Jul 2018

The Impairment of TorsinA's Binding to and Interactions With Its Activator: An Atomistic Molecular Dynamics Study of Primary Dystonia

in Biological Modeling and Simulation

Emmanuel O. Salawu

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2018.00064

3,497 views
17 citations

Original Research

Published on 11 Jun 2018

Are Amyloid Fibrils RNA-Traps? A Molecular Dynamics Perspective

in Biological Modeling and Simulation

Massimiliano Meli
Maria Gasset
Giorgio Colombo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2018.00053

3,412 views
4 citations

Original Research

Published on 15 Jun 2017

New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis

in Biological Modeling and Simulation

Marco Fantini
Duccio Malinverni
Paolo De Los Rios
Annalisa Pastore

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2017.00040

5,259 views
7 citations

Original Research

Published on 11 Jan 2016

Atomic Coordination Reflects Peptide Immunogenicity

in Biological Modeling and Simulation

Georgios S. E. Antipas
Anastasios E. Germenis

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2015.00077

3,363 views
5 citations

Perspective

Published on 21 Aug 2015

Current theoretical models fail to predict the topological complexity of the human genome

in Biological Modeling and Simulation

Javier Arsuaga
Reyka G Jayasinghe
Robert G. Scharein
Mark R Segal
Robert Stolz
Mariel Vazquez

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2015.00048

6,496 views
16 citations

Perspective

Published on 27 May 2015

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

in Biological Modeling and Simulation

Elena Papaleo

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2015.00028

9,076 views
61 citations

Hypothesis and Theory

Published on 28 Apr 2015

Elements of the cellular metabolic structure

in Biological Modeling and Simulation

Ildefonso M. De la Fuente

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2015.00016

40,580 views
40 citations

Navigation group

Articles

Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase

Building Minimalist Models for Functionalized Metal Nanoparticles

Using Dimensionality Reduction to Analyze Protein Trajectories

Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods

Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

The Impairment of TorsinA's Binding to and Interactions With Its Activator: An Atomistic Molecular Dynamics Study of Primary Dystonia

Are Amyloid Fibrils RNA-Traps? A Molecular Dynamics Perspective

New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis

Atomic Coordination Reflects Peptide Immunogenicity

Current theoretical models fail to predict the topological complexity of the human genome

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

Elements of the cellular metabolic structure