Frontiers in Molecular Biosciences | Biological Modeling and Simulation

Perspective

Published on 04 Dec 2019

Accurate Biomolecular Simulations Account for Electronic Polarization

in Biological Modeling and Simulation

Josef Melcr
Jean-Philip Piquemal

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00143

9,759 views
64 citations

Original Research

Published on 28 Nov 2019

Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

in Biological Modeling and Simulation

Zane R. Thornburg
Marcelo C. R. Melo
David Bianchi
Troy A. Brier
Cole Crotty
Marian Breuer
Hamilton O. Smith
Clyde A. Hutchison
John I. Glass
Zaida Luthey-Schulten

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00130

8,211 views
21 citations

Opinion

Published on 15 Nov 2019

Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes

in Biological Modeling and Simulation

Angelo Rosa
Marco Di Stefano
Cristian Micheletti

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00127

4,047 views
15 citations

Opinion

Published on 13 Nov 2019

To Bud or Not to Bud: A Perspective on Molecular Simulations of Lipid Droplet Budding

in Biological Modeling and Simulation

Valeria Zoni
Vincent Nieto
Laura J. Endter
Herre J. Risselada
Luca Monticelli
Stefano Vanni

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00124

4,864 views
33 citations

Review

Published on 05 Nov 2019

Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier

in Biological Modeling and Simulation

Laura Orellana

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00117

29,765 views
114 citations

Brief Research Report

Published on 30 Oct 2019

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

in Biological Modeling and Simulation

Jinan Wang
Andrey Alekseenko
Dima Kozakov
Yinglong Miao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00112

24,875 views
90 citations

Opinion

Published on 30 Oct 2019

Multiscale Solutions to Quantitative Systems Biology Models

in Biological Modeling and Simulation

Nehemiah T. Zewde

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00119

3,562 views
5 citations

Brief Research Report

Published on 17 Oct 2019

Enzymatic Polymerization of PCL-PEG Co-polymers for Biomedical Applications

in Biological Modeling and Simulation

Pedro Figueiredo
Beatriz C. Almeida
Alexandra T. P. Carvalho

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00109

5,088 views
12 citations

Brief Research Report

Published on 15 Oct 2019

Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin

in Biological Modeling and Simulation

Francesco Delfino
Yuri Porozov
Eugene Stepanov
Gaik Tamazian
Valentina Tozzini

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00104

4,062 views
8 citations

Brief Research Report

Published on 02 Oct 2019

Definition of the Minimal Contents for the Molecular Simulation of the Yeast Cytoplasm

in Biological Modeling and Simulation

Vijay Phanindra Srikanth Kompella
Ian Stansfield
Maria Carmen Romano
Ricardo L. Mancera

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00097

4,324 views
2 citations

Technology and Code

Published on 01 Oct 2019

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing

in Biological Modeling and Simulation

Rodrigo V. Honorato
Jorge Roel-Touris
Alexandre M. J. J. Bonvin

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00102

13,744 views
34 citations

Original Research

Published on 01 Oct 2019

The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus

in Biological Modeling and Simulation

Havva Yalinca
Charlotte Julie Caroline Gehin
Vladimiras Oleinikovas
Hilal A. Lashuel
Francesco Luigi Gervasio
Annalisa Pastore

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00095

5,902 views
24 citations

Brief Research Report

Published on 27 Sep 2019

Global Dynamics of Yeast Hsp90 Middle and C-Terminal Dimer Studied by Advanced Sampling Simulations

in Biological Modeling and Simulation

Florian Kandzia
Katja Ostermeir
Martin Zacharias

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00093

2,974 views
6 citations

Mini Review

Published on 11 Sep 2019

Modeling Crowded Environment in Molecular Simulations

in Biological Modeling and Simulation

Natalia Ostrowska
Michael Feig
Joanna Trylska

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00086

9,900 views
48 citations

Opinion

Published on 10 Sep 2019

Some Notes on the Thermodynamic Accuracy of Coarse-Grained Models

in Biological Modeling and Simulation

Ewa Anna Oprzeska-Zingrebe
Jens Smiatek

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00087

3,378 views
5 citations

Editorial

Published on 29 Aug 2019

Editorial: Machine Learning in Biomolecular Simulations

in Biological Modeling and Simulation

Gennady Verkhivker
Vojtech Spiwok
Francesco Luigi Gervasio

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00076

4,584 views
4 citations

Original Research

Published on 13 Aug 2019

Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins

in Biological Modeling and Simulation

Omar Demerdash
Utsab R. Shrestha
Loukas Petridis
Jeremy C. Smith
Julie C. Mitchell
Arvind Ramanathan

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00064

7,374 views
30 citations

Mini Review

Published on 09 Aug 2019

Computational Studies of Cardiac and Skeletal Troponin

in Biological Modeling and Simulation

Jacob D. Bowman
Steffen Lindert

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00068

7,315 views
27 citations

Opinion

Published on 06 Aug 2019

Unraveling the Molecular Mechanism of Pre-mRNA Splicing From Multi-Scale Simulations

in Biological Modeling and Simulation

Lorenzo Casalino
Alessandra Magistrato

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00062

3,521 views
7 citations

Perspective

Published on 23 Jul 2019

A Multi-Scale Approach to Membrane Remodeling Processes

in Biological Modeling and Simulation

Weria Pezeshkian
Melanie König
Siewert J. Marrink
John H. Ipsen

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00059

6,723 views
26 citations

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

6,064 views
23 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

3,608 views
10 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

15,934 views
80 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

7,678 views
31 citations