Dynamic Interactions Between Biomolecules: Insights from Bioinformatics and Computational Biology

Dear Colleagues,

Dynamic interactions between biomolecules, including proteins, nucleic acids, lipids, carbohydrates, and small molecules, are fundamental to biological functions, regulations, and disease mechanisms. Processes such as molecular recognition, allosteric regulation, signaling, and complex assembly are not only governed by molecular structure, but also by conformational flexibility, interaction kinetics, and environmental contexts. While experimental approaches provide invaluable insights, they often capture static or ensemble-averaged representations that incompletely describe the dynamic nature of biomolecular systems.

Recent advances in bioinformatics, computational biology, molecular simulations, and artificial intelligence have significantly expanded our ability to investigate biomolecular interactions across spatial and temporal scales. These approaches enable the integrative analysis of large-scale biological data, the high-resolution modeling of molecular dynamics, and the predictive understanding of interaction mechanisms, thereby complementing experimental studies and advancing biomolecular research.

We are pleased to invite you to contribute to this Special Issue of Biomolecules, which will focus on computational and data-driven approaches to understanding dynamic biomolecular interactions.

This Special Issue aims to bring together original research and review articles that elucidate the structure–function–dynamics relationships between biomolecules using computational and bioinformatics methodologies. This topic is fully aligned with the scope of Biomolecules, which emphasizes molecular mechanisms, structural and functional characterization, and theoretical and computational studies of biological macromolecules. By highlighting methodological innovations and biologically relevant applications, this Special Issue seeks to provide a coherent collection of high-quality contributions that advance our understanding of biomolecular dynamics in health, disease, and biotechnology.

In this Special Issue, original research articles and reviews are welcome. Research areas may include, but are not limited to, the following:

• Molecular dynamics simulations and enhanced sampling techniques;
• Protein–protein, protein–nucleic acid, and protein–ligand interactions;
• Structural bioinformatics and integrative or hybrid modeling approaches;
• Conformational dynamics, allostery, and intrinsically disordered biomolecules;
• Computational analysis of biomolecular complexes and assemblies;
• Machine learning- and AI-based methods for interaction prediction and dynamics;
• Multi-omics data integration for studying molecular interactions;
• Reproducible workflows and computational platforms for biomolecular research.

We look forward to receiving your contributions to this Special Issue.

Dr. Jayadev Joshi
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 250 words) can be sent to the Editorial Office for assessment.

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.

• biomolecular interactions
• molecular dynamics
• structural bioinformatics
• computational biology
• protein interactions
• conformational dynamics
• machine learning
• systems biology
• integrative modeling
• drug discovery