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Special Issue "Protein Dynamics Simulations"
A special issue of Biomolecules (ISSN 2218-273X).
Deadline for manuscript submissions: closed (1 August 2019).
Over the past 50 years, the simulation of proteins has experienced transformative growth due to advances in computational technology. GPU computing has allowed biological molecules to be simulated for longer times, enabling the investigation of long-range conformational changes that were previously inaccessible. As computational power has increased, simulation techniques such as accelerated molecular dynamics have enabled longer simulations of larger, more complex biological systems. For example, simulations of protein–nucleic acid complexes such as CRISPR-Cas9 now offer unprecedented access to the atomic details of intricate enzymatic reactions.
In addition to advances in computer hardware and simulation techniques, the emergence of high-resolution cryo-EM data over the past decade has ushered in a new era of the investigation of larger membrane-bound proteins. As these proteins are often the target of small-molecule drugs, the elucidation of their structure is the first step to understanding their complex functionality. Protein dynamics simulations based on cryo-EM data will offer further insight into the machinery of these membrane-bound proteins.
This Special Issue on protein dynamics simulations welcomes contributions that highlight method development as well as applications to novel biological systems. Relevant topics may include protein–ligand interactions (e.g., in the context of drug discovery and translational medicine), docking techniques, calculation of binding free energies, advances in developing polarizable force fields, hybrid quantum mechanical/molecular mechanical (QM/MM) MD approaches, development and improvement of force fields for biomolecules, coarse-grained models, solvation models, simulation of radiation–matter interactions, and enzymatic catalysis.
Research articles as well as reviews are welcome. We look forward to your contribution.
Dr. Nadia Elghobashi-Meinhardt
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 1200 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.
- protein–ligand interactions
- molecular modeling and simulations
- homology modeling
- docking techniques
- free-binding energy calculation
- advances in developing polarizable force fields
- coarse-grained models
- solvation models
- simulation of radiation-matter interactions
- enzymatic catalysis