HDXmodeller returns residue resolved HDX protection factors from low resolution peptide data typical of HDX-MS. The program also returns a range of important statistical outputs for post-optimisation data validation. The use of HDXmodeller requires site registration after which a unique username and password will be provided. HDXmodeller requires the following two input .txt files:

File 1 should report the relative fractional uptake (RFU) of each peptide at each labelling time point along with the amino acid sequence of each peptide and their start and end positions within the protein. Users should ensure that the RFU have been corrected for extraneous exchange prior to optimisation. Data that has not been corrected for back and forward exchange is likely to result in erroneous results. For best results please report all RFU to 6-decimal places to compliment the precision of HDXmodeller. Data to this level of precision can be created upon correction for extraneous exchange. Please note that HDXmodeller accepts both tab and space delineated data.

File 2 should report the intrinsic exchange rate constant(kint) of each amino acid calculated at the temperature and pD for which the HDX-MS experiments were performed. For preparation of kint text files we recommend that users utilise our kint calculation tool located in the HDXutilities workspace.

File 3 (optional) an optional constraint file can be added for 2-stage optimisation. The file labelled "Const_gen_..." should be uploaded to apply a fixed constraint of +/- 2 lnP to specified amino acids. Note, constraint files can only be used if they have been outputted from an optimisation involving a minimum of 50 replicates. Optimisation performed with constraints should also be limited to a minimum of 50 replicates and interpreted by comparison of the respective R-matrix scores of the 2 optimisations (please refer to article entitled "Exploiting the propagation of constrained variables for enhanced HDX-MS data optimisation" and cite this article for any use of the constraint feature of HDXmodeller.

Users should refer to the example data provided for guidance on the correct layout of input data.
All calculations should be performed with default settings except for evaluation runs for which the number of replicates should be reduced to 10. A project name and an address to where the results will be emailed following optimisation must also be provided prior to the execution of the run initiated using the “Submit” button.
All registered users are limited to 6 submissions / day.
For support please email hdxsite@gmail.com