Molecular Dynamics Simulations and Structural Analysis of Protein Domains (2nd Edition)
A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".
Deadline for manuscript submissions: 31 January 2025 | Viewed by 50
Special Issue Editor
Interests: structural bioinformatics; bioinformatics; next-generation sequence; drug design; deep learning
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
The 3D structure of proteins is the basis for all their biological functions. For more than 50 years, obtaining this structure has been difficult, costly and sometimes impossible. Molecular modelling approaches are therefore making it possible to increase our knowledge by providing high-quality 3D structural models. In this context, the AlphaFold2 deep learning approach has enabled significant progress, with hundreds of millions of 3D structural models being made available to the scientific community.
However, the 3D structure gives only a small insight into biological function. The 3D structure or 3D model is static, whereas the different parts of proteins are rigid, flexible, highly flexible or even completely disordered. Similarly, biological function can be associated with major conformational changes that are not provided by knowledge of a single structure. It is therefore essential to understand the life of protein structures through their dynamics. Molecular dynamics simulations (DMs), both classical and advanced, provide access to much more detailed questions of critical biomedical interest. For example, a point mutation in a structural model does not explain the functional change at the atomic level. Molecular dynamics simulations are needed to generate hypotheses about the effects of these variants. In this way, DMs allow us to see allosteric changes that are sometimes impossible to characterise experimentally.
This Special Issue will therefore focus on issues ranging from the most fundamental to the most applied research on protein structures (or structural models), through the use and/or development of both classical and more innovative simulations. It can start with the construction of a model or the use of a 3D structure and then its analysis by DMs, the comparison between different variants, the question of the binding of ligands or proteins of interest, etc.
Dr. Alexandre G. De Brevern
Guest Editor
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Keywords
- protein structures
- molecular dynamics
- advanced molecular dynamics
- variants
- pathologies
- drug design
- allostery
- protein domains
- secondary structures
- methodological development
- protein design
- ligands
- normal mode analysis
- machine learning
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