Computational Analysis and Conformational Modeling for Protein Structure and Interaction

Dear Colleagues,

Protein structure and interaction are fundamental aspects of molecular biology and biochemistry, playing crucial roles in various biological processes, notably, signal transduction, molecular recognition, and enzymatic reactions. Understanding protein structure and interaction is essential for elucidating the molecular mechanisms underlying biological processes, designing new therapeutic agents, and engineering proteins with desired functions. Experimental techniques such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM), and most recently, deep learning-based methods such as AlphaFold2, ESMFold, and RosettaFold, are commonly used to study protein structure and characterization. However, these techniques are notably limited by their inability to elucidate the atomistic-level conformational dynamics associated with protein interaction. To address this limitation, computational analysis and conformational modeling present powerful tools for analyzing protein structures, predicting their conformational dynamics, and elucidating their interactions. Augmenting experimental methods, computational analysis, and conformational modeling techniques unravel crucial structural insights that further our understanding of protein structure and interactions.

This Special Issue highlights and disseminates cutting-edge research in computational analysis and conformational modeling of protein structure and interaction. Thematic areas of interest include, but are not limited to, the following:

1. Strengths and limitations of current computational analysis and conformational modeling techniques for investigating protein structure and interaction.
2. Molecular dynamics simulations and computational modeling to explore protein dynamics and conformational changes.
3. Molecular docking and molecular modeling techniques for studying protein–protein, protein–peptide, and protein–small molecule interactions.
4. Applications of computational methods in drug discovery and design targeting protein–protein interactions.
5. Integration of experimental and computational approaches to validate protein structures and interactions and to also provide a comprehensive understanding of protein dynamics and function.
6. Artificial intelligence and machine learning-based approaches for predicting protein structure, functions, interactions, and conformational analysis.

We cordially invite investigators to contribute high-quality original research and review articles that cover any relevant topics that advance our understanding of protein structure and interaction through computational analysis and modeling. By bringing together diverse perspectives and methodologies, this Special Issue aims to drive innovation in the field and facilitate the development of new therapeutic strategies targeting protein function and interaction.

Dr. Clement Agoni
Dr. Indrani Bera
Guest Editors

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. 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 2700 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 structure prediction
• drug discovery targeting proteins
• structural bioinformatics
• molecular dynamics simulations
• protein–protein interactions
• protein–ligand binding
• conformational dynamics
• molecular docking studies