Computational Chemical Biology: Recent Advances and Future Trends
A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".
Deadline for manuscript submissions: 30 September 2025 | Viewed by 24
Special Issue Editors
Interests: drug design; molecular dynamics simulations; G protein-coupled receptors; allostery; allosteric mechanisms
Special Issues, Collections and Topics in MDPI journals
Interests: biomolecular simulations; drug design; cryptic site identification and prediction; enhanced sampling methods
Special Issue Information
Dear Colleagues,
The field of computational chemical biology is undergoing a transformative era, driven by breakthroughs in artificial intelligence, multi-scale modeling, and integrative omics. Firstly, it is well known that computational chemical biology is experiencing a paradigm shift, fueled by artificial intelligence, such as deep learning models that predict protein–ligand binding affinities and a recent diffusion model that designs novel therapeutics. These advancements could potentially accelerate the shift from traditional trial-and-error to rational drug design and shorten drug discovery timelines from years to months. Meanwhile, multi-scale modeling techniques that bridge quantum mechanical simulations of enzyme active sites to coarse-grained analyses of cellular-scale processes help us to gain valuable insights into the atomistic details of drug binding and biomolecular functions and promote the rational design of precision medicines. Boosted by easy access to an increasing amount of bioinformatics data, integrative omics has attracted great attention for leveraging machine learning to synthesize genomics, proteomics, and metabolomics data into actionable insights. These innovations are reshaping drug discovery, protein engineering, and our understanding of complex biological systems. As Guest Editors of this Special Issue, we invite you to contribute original research, reviews, and perspectives that highlight cutting-edge developments at the intersection of computation, chemistry, and biology.
Scope and Themes
This Special Issue is focused on interdisciplinary approaches addressing pressing challenges in drug development, biomedicine, and biotechnology. Topics of interest include, but are not limited to, the following:
- AI-Driven Molecular Design: Generative models, reinforcement learning, and transformer-based tools for drug discovery, protein engineering, and CRISPR guide design.
- Structure-Based Innovations: Advances in molecular docking, free-energy calculations, and applications of AlphaFold/RoseTTAFold in target identification.
- Multi-Scale Modeling: Quantum mechanics/molecular mechanics (QMs/MMs), coarse-grained simulations, and enhanced sampling techniques for studying biomolecular dynamics.
- Omics and Systems Biology: Integrative chemoproteomics, metabolomics, and network pharmacology for unraveling disease mechanisms.
Prof. Dr. Shaoyong Lu
Guest Editor
Dr. Jianxiang Huang
Guest Editor Assistant
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. Molecules is an international peer-reviewed open access semimonthly 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.
Keywords
- machine learning/deep learning in drug discovery
- multi-scale simulations and MD and QM/MM simulations
- biomolecular conformational changes and allostery
- systems and network pharmacology
- chemical library screening and cheminformatics
- bioinformatics integration and big data in drug discovery
- ADMET prediction and drug repurposing
- target prediction/validation and hit-to-lead optimization
Benefits of Publishing in a Special Issue
- Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
- Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
- Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
- External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
- e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.
Further information on MDPI's Special Issue policies can be found here.
