Computational Modeling of Structure and Function of Biomolecules
A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Biology".
Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 5221
Special Issue Editor
Interests: computer aided design of multifunctional peptides; protein structure–function relationship by network analysis
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
In 2020, we witnessed the first solution that predicted the atomic three-dimensional structure of proteins and matched the reliability of experimental methods at the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. The impact of this scientific achievement will influence the protein field and the biology discipline in the coming years. For instance, while most common computational tools to predict protein function are based on protein sequence, this may change and be improved by having access to reliable three-dimensional models, and there are plenty of proteins that may benefit from this: in the last release of UniProt database (2020_06) there were 563,972 entries and only 5.27% of these have an entry in the Protein Data Bank. Thus, it is expected that computational tools using, generating, storing, or classifying structural models of proteins will become more common.
Proteins may be stably structured, metamorphic, or intrinsically disordered. Understanding the structural differences that generate this diversity and their impact on the function of proteins remains an open area of research in the field. The basic question as to how many different protein folds exist has evolutionary implications. Furthermore, proteins usually associate with other molecules to exert their functions, and these interactions usually induce structural and functional changes that are still not well understood. However, the advances in the protein structure modeling field may also have an impact on the understanding of other biomolecules, such as RNA, DNA, carbohydrates, and lipids. For instance, they may inspire the generation of more reliable structural models of these polymers or may facilitate modeling the interactions between these molecules and proteins. Most reliable models of protein structure and function involve some form of artificial intelligence, including but not limited to machine learning and deep learning.
Motivated by these possibilities, we invite the computational community to contribute their work to this Special Issue on “Computational Modeling of Structure and Function of Biomolecules”. This issue is centered around computational modeling of protein structures or proteins in complex with any other biomolecules and seeks work that sheds light on protein structure prediction, folding, structural transitions, protein interactions, and allostery, among others. This modeling may include but is not limited to the following techniques:
- Machine learning;
- Deep learning;
- Statistical analysis;
- Geometrical analysis;
- Graph theory;
- Physics-based approaches;
- Phylogeny-based approaches.
Dr. Gabriel Del Río Guerra
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 submissions that pass pre-check are 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. Computation 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 1800 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 structure
- Protein function
- Computational model
- Prediction
- Artificial intelligence
