Background During the course of most infections, the initial fever response from the host is beneficial in clearing out pathogens. The role of febrile temperatures on the stability and activity of antibodies raised against various viral, bacterial and protozoan targets is yet unknown. Objective To produce Molecular Dynamics trajectories of immune complexes formed by monoclonal antibodies against antigens from protozoans and against targets relevant for allergies, at pertinent temperatures (310–313 K). Materials and methods We used the RCSB database to identify 38 antibody: antigen complexes of interest, and set up GROMACS to prepare, run and analyze these structures at different temperatures for 100–500 ns, in single or multiple random seeds. Results We provide a major update to our previous database (doi: <a href="https://doi.org/10.1093/database/baae015">https://doi.org/10.1093/database/baae015</a>) with new PDB entries and additional processed data that include Root Mean Square Deviations, Root Mean Square Fluctuations, Solvent-accessible surface area, H-bonds, Radii of gyration and some additional free binding energy calculations for existing Molecular Dynamics trajectories, at different temperatures. We further added new Molecular Dynamics trajectories relevant for infections and allergies with similar outputs and additional PDB structures obtained every 50 ns. Each piece of data is associated to a unique DOI. We make use of the same web interface, ThermoPCD, as a platform to centralize and link all data to our repository [<a href="https://dataverse.harvard.edu/dataverse/ThermoPCD">https://dataverse.harvard.edu/dataverse/ThermoPCD</a>] on Harvard Dataverse [<a href="https://dataverse.harvard.edu">https://dataverse.harvard.edu</a>]. Testable hypotheses ThermoPCD 2.0 data allow users to understand patterns of temperature activation in a physiological range in antibodies that may affect their structure and functions, and relate these outputs to their own experimentally derived binding affinities. Conclusion ThermoPCD is a free to use database containing Molecular Dynamics trajectories of immune complexes obtained at physiologic and febrile temperatures, that allows unrestricted access and complete data download without registration. Database URL: <a href="https://sites.google.com/view/thermopcd/home">https://sites.google.com/view/thermopcd/home</a>.

ThermoPCD 2.0: an updated database of molecular dynamics trajectories of antibody-antigen complexes relevant for infectious diseases and allergies at physiologic and fever-range temperatures

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2025年11月26日

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Puneet K. Singh,
Mohammad Karbalaeimahdi,
Razvan C. Stan

摘要

Background

During the course of most infections, the initial fever response from the host is beneficial in clearing out pathogens. The role of febrile temperatures on the stability and activity of antibodies raised against various viral, bacterial and protozoan targets is yet unknown.

Objective

To produce Molecular Dynamics trajectories of immune complexes formed by monoclonal antibodies against antigens from protozoans and against targets relevant for allergies, at pertinent temperatures (310–313 K).

Materials and methods

We used the RCSB database to identify 38 antibody: antigen complexes of interest, and set up GROMACS to prepare, run and analyze these structures at different temperatures for 100–500 ns, in single or multiple random seeds.

Results

We provide a major update to our previous database (doi: https://doi.org/10.1093/database/baae015) with new PDB entries and additional processed data that include Root Mean Square Deviations, Root Mean Square Fluctuations, Solvent-accessible surface area, H-bonds, Radii of gyration and some additional free binding energy calculations for existing Molecular Dynamics trajectories, at different temperatures. We further added new Molecular Dynamics trajectories relevant for infections and allergies with similar outputs and additional PDB structures obtained every 50 ns. Each piece of data is associated to a unique DOI. We make use of the same web interface, ThermoPCD, as a platform to centralize and link all data to our repository [https://dataverse.harvard.edu/dataverse/ThermoPCD] on Harvard Dataverse [https://dataverse.harvard.edu].

Testable hypotheses

ThermoPCD 2.0 data allow users to understand patterns of temperature activation in a physiological range in antibodies that may affect their structure and functions, and relate these outputs to their own experimentally derived binding affinities.

Conclusion

ThermoPCD is a free to use database containing Molecular Dynamics trajectories of immune complexes obtained at physiologic and febrile temperatures, that allows unrestricted access and complete data download without registration. Database URL: https://sites.google.com/view/thermopcd/home.