In inflamed tissues, a range of modifications in the physical and chemical conditions occur that may affect the subsequent immune responses. Among these, changes in pH and hypoxia are important, as are the variations in the local  temperature. 

We seek to determine the role of core body temperature (37°C) and fever-range temperatures (38°C - 40°C) on the adaptive immunity response, and in some instances, at 25°C. We here focus on the immune complexes formed by antibodies against antigens from different cancer models, autoimmune diseases, infections and, as controls, allergic conditions. First, as autoimmunity may lead to chronic inflammation and in turn to favoring the growth of various tumors, it is important to determine what the role of pertinent temperatures is on the stability and the binding affinities of autoantibodies, and of therapeutic antibodies. Second, fever is an evolutionarily conserved and largely beneficial physiologic reaction to the presence of pathogens. By focusing on some of the most common antigen targets, we aim to reveal the connection between inflammation temperatures versus in tumor biology and autoimmunity on one hand, and additional roles for fever during infections, on the other hand.

Although full atomic molecular dynamics (MD) simulations for large systems, as with antibody:antigen complexes, are key for elucidating the atomic details of their interactions, these are time and cost-prohibitive. Furthermore, such MD trajectories are usually run for short periods (10 ns to tens of nanoseconds), commonly at single temperature points and in single trajectories. We release here datasets of trajectories of immune complexes, including a list of antigens or antibodies only, at 3-5 temperature values, over a 100 ns to 500 ns range, of single or multiple independent runs. 

Users can freely avail of the data. All raw and processed data, that includes RMSD, RMSF, Rg, H-bonds and SASA, is stored on Harvard Dataverse repository at ThermoPCD - Dataverse (harvard.edu). Users can retrieve the data directly from Dataverse using the search fields present on the pages that list all PDB entries for each category (Cancers, Autoimmunity, Pathogens and Allergies), or search this website to obtain the relevant links and more information about a particular PDB (eg. presence of mutations, epitope and paratope residues etc).  To obtain the .xtc files etc, use the contact details below.

To quote this work in a publication, use the following reference:

Singh PK, Stan RC. ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. Database (Oxford). 2024 Mar 19; 2024:baae015. doi: 10.1093/database/baae015.