Special Issue "Molecular Dynamics Simulations"
Deadline for manuscript submissions: closed (31 December 2018).
Interests: Methodology in computational structural biology; molecular modeling of protein systems; protein-protein and protein-ligand interactions; molecular dynamics of protein-ligand complexes; binding free energies in protein-ligand complexes; electrostatic potentials and protein surfaces; quantum calculations of structures and properties of ligands
Interests: Characterization of allergen proteins; structure and molecular properties of allergens; protein-ligand complexes in immunological processes associated to sensitization to allergens; food allergy; molecular dynamics of allergens; protein-ligand docking in allergen systems
New developments in X-ray crystallography, fiber diffraction, solid state nuclear magnetic resonance, and cryo-electron microscopy have permitted considerable advances in the determination of biomolecular structures in recent years. However, these structures provide a static view that frequently lack key data to fully understand molecular mechanisms and functions. Molecules are live entities, their atoms are in constant motion interacting with the environment and other molecules, and a dynamic view is needed to study their behavior. Molecular Dynamics (MD) simulations, nowadays, allow to explore time-dependent changes occurring in molecular systems thus providing paramount information to understand a wide range of chemical and biological phenomena. Advances in algorithms, software, and computer technology regarding high-performance computing and GPU-based processing in the last decade have resulted in a giant step forward in MD simulations on complex large molecular systems. In many cases, MD can be viewed as a counterpart to experiment as MD data frequently help interpret in vivo and in vitro results and are invaluable in proposing hypotheses and experiments.
This Special Issue on “Molecular Dynamics Simulations” is open to researchers working with Molecular Dynamics at any level. Papers addressing methodological or computational developments on force field effects, full-atom/coarse grained calculations, explicit/implicit treatment of solvent, analyses of trajectories, etc., as well as papers reporting applications to diverse molecular systems, interactions, protein function, etc., are welcome. Submission of up-to-date review articles is also encouraged.
Prof. Dr. Luis F. Pacios
Dr. María Garrido-Arandia
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.
- Dynamic effects in molecules
- Dynamic changes of intermolecular interactions
- Structure-function relationships in proteins
- Protein-ligand interactions
- Nucleic acid ligand interactions
- Computational modeling of molecular systems
- Drug design