Computational Biophysics in Understanding the Molecular Function of Pathogens

Dear Colleagues,

Computational biophysics has become a pivotal tool used to address complex biological challenges posed by pathogens and infections. Advanced computational techniques are being applied across various domains, including simulating biomolecular interactions, understanding pathogen–host dynamics, and designing antiviral drugs. For this Special Issue, we encourage submissions that showcase novel algorithms and methodologies, including, but not limited to, molecular dynamic simulations, coarse-grained modeling, and integrative approaches applied to pathogenic data. Techniques such as quantum mechanical/molecular mechanical (QM/MM) modeling, Markov state models, and machine learning approaches are also welcome to be focused on, particularly in terms of their role in elucidating detailed mechanistic insights. Studies that integrate computational tools with experimental data, such as cryo-EM, NMR spectroscopy, and X-ray crystallography, to provide comprehensive solutions to pathogen-related questions are encouraged to be submitted. Also, contributions exploring the use of big data, clinical datasets, and experimental data for training and validating computational models are welcomed. This Special Issue aims to explore the latest discoveries that bridge computational methodologies with biological insights, advancing our understanding of pathogens and infections, and informing the development of novel therapeutic strategies. We look forward to receiving your valuable contributions to this critical area of computational biophysics in the study of pathogens and infections.

Original papers and high-quality review articles are welcome to be submitted to this Special Issue. Potential topics include, but are not limited to, the following:

• Molecular dynamic simulations of pathogen–host interactions;
• Machine learning approaches in predicting pathogen virulence;
• Quantum mechanical/molecular mechanical (QM/MM) modeling of viral proteins;
• Big data analytics for epidemiological modeling of infectious diseases;
• Integrative structural biology using cryo-EM and computational tools;
• Computational design of antiviral and antibacterial therapeutics.

Dr. Wenhan Guo
Dr. Lin Li
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. Pathogens 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 2200 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.

• pathogen–host interactions
• structural biology
• therapeutic design
• molecular dynamic simulations
• machine learning