Latest Advances in Molecular Docking Involved in Biophysics
A special issue of Biophysica (ISSN 2673-4125).
Deadline for manuscript submissions: 31 August 2026 | Viewed by 26
Special Issue Editor
Special Issue Information
Dear Colleagues,
Molecular docking is a fundamental method in computational biophysics and plays an indispensable role for the study of physical principles of biomolecular recognition as well as assembly. This Special Issue is centered on conceptual and methodological developments concerning molecular docking with a biophysical approach. These contributions represent advances in protein–ligand, protein–protein, and protein–nucleic acid interactions and integrative approaches that integrate docking with molecular dynamics simulations and multiscale modeling efforts to connect structure, dynamics, and biological function.
Applications to drug design-type problems are given as test cases for biophysical simulation in which quantitative estimates of binding modes, thermodynamic contributions, and kinetic pathways can be determined. The greater coupling between machine learning methods and free-energy calculations has not only extended the range of applications of docking methodologies, but it has also provided new knowledge on the physics behind molecular affinity and selectivity.
The role of QM approaches, such as density functional theory (DFT), in providing an improved representation on top of docking-based models is also discussed. By allowing for rigorous characterization of electronic interactions, polarization effects, and spectroscopic observables, DFT-based methods help advance our understanding of biomolecular interactions and establish the realm where classical force-field approximations become inaccurate.
Lastly, this Special Issue touches upon major open questions in molecular docking for biophysics, such as experimental verification, consistency between models on different scales, and reproducibility. This issue seeks to gather a collection of theoretical, methodological, and application-focused studies that offer a coherent and prospective view on the state-of-the-art as well as future trends of molecular docking in biophysics.
Dr. Mohammed Bouachrine
Guest Editor
Manuscript Submission Information
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Keywords
- molecular docking
- biophysical simulation
- protein–ligand interactions
- protein–protein interactions
- protein–nucleic acid interactions
- free-energy calculations
- machine learning
- density functional theory (DFT)
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