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HDX Energy

Creator Names:

  • Tung Nguyen
  • Daniel Marzolf
  • Justin Seffernick
  • Sten Heinze
  • PI: Steffen Lindert (lindert.1@osu.edu)

Date created: February 22, 2022

Use Hydrogen-deuterium exchange (HDX) data measured by nuclear magnetic resonance (NMR) to evaluate protein structural information and to supplemented computational prediction methods with a scoring function to quantify the agreement with HDX data.

Reference: https://doi.org/10.1016/j.str.2021.10.006

Categorical

Use strength categories that corresponded to HDX rates (rather than the quantitative exchange rates) to score.

Quantitative

Use quantitative protection factors (PFs) from HDX-NMR for scoring.

Usage

To use the application, the following command line options can be specified:

-in:file:s 1a2p_A.pdb
-in::file::HDX 1a2p_pf.txt
-ResPF
-out::file::o 1a2p_test.out

Example

./HDXEnergy.linuxgccrelease -in:file:s 1a2p_A.pdb -in::file::HDX 1a2p_pf.txt -out::file::o 1a2p_test.out -ResPF