Special Issue "Protein Dynamics: New Advanced Computing Methods and Tools"

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules".

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editor

Prof. Luba Tchertanov
Website
Guest Editor
Université Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, 4 av. des Sciences, F-91190 Gif-sur-Yvette, France
Interests: computational structural biology; biophysics; machine learning; molecular dynamics; receptors; post-translational modifications; allosteric regulation

Special Issue Information

Protein functions are closely associated with internal motions occurring over a wide range of time scales, from atomistic vibrations to global motions (e.g., large-scale conformational transitions), ranging from fs to ms or a longer timescale. Simulation of molecular dynamics is a technique that applies the laws of physics to a protein 3D structure to predict the time-dependent evolution of interacting particle systems.

Such a simulation provides access to complex data and models and enables understanding at the atomic level of dynamic processes in cells−signal transduction, transcription control, motor work, channel gating, enzyme catalysis, molecular recognition, and allosteric regulation.

A route from 3D structure to biofunctions is a connected sequence of different computational stepping-stones—the generation of high-throughput data, post-processing of these data, data analysis, and comprehensive graphical representation.  

This Special Issue aims to highlight new methods and/or software tools targeting both the generation of reliable data for highly flexible and large proteins (in particular membrane proteins, intrinsically disordered proteins, etc.) under controlled computational resources, as well as a comprehensive data exploration and rigorous representation of results.

This Special Issue aims to highlight new methods and/or software tools targeting both the generation of reliable data (from quantum to coarse-grained models, classical or accelerated techniques) for highly flexible and large proteins (in particular membrane proteins and/or intrinsically disordered proteins) under specific controlled computing resources, a full exploration of these data, and rigorous representation of the results.

Special Issue Information

Dear Colleagues,

Biomolecules (Impact factor 4.082; https://www.mdpi.com/journal/biomolecules) has elected computing tools for the description of protein dynamics as the focus of a forthcoming Special Issue. The aim is to gather impactful research papers and reviews under the specific topic of “Advanced Analysis of Protein Dynamics ". In this Special Issue, published as an open-access collection of articles, Dr. Luba Tchertanov will take on editorial responsibility. 

As a key researcher working in this exciting area, we invite you to contribute to this Special Issue. We believe that your work would make an excellent contribution and greatly increase the issue’s impact. The scope of the issue is detailed fully at the dedicated webpage: 

We intend to publish your manuscript as an invited ‘Featured Article’, which means that your submission will be handled on a priority basis and may be chosen as the cover story of the forthcoming issue.

The deadline for the manuscript submission is 31 December 2021. However, we would be delighted to receive your positive response and a tentative title at the earliest convenient time by answering directly to this email ([email protected]).

Authors are invited to submit original research and review papers addressing topics related to the scope of this Special Issue. You may share this invitation with your team members and colleagues; student co-authors are most welcome. It will be exciting to hear about your participation.

We look forward to your reply!

Kind regards, 

Prof. Luba Tchertanov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Protein Dynamics
  • Molecular Dynamics Algorithms
  • Potentials in MD Simulations
  • Data Processing
  • Data Analysis
  • Free Energy Landscape
  • Communication Pathway
  • Visualisation and Graphics
  • Highly Flexible Proteins
  • Intrinsically Disordered Proteins
  • Metastable States

Published Papers

This special issue is now open for submission.
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