In NMR studies of proteins it is useful to have the probability of NOESY contacts between two protons.
We have developed a module for validating chemical shifts assignments against NOESY data (ARECA),
and as a part of this module we calculated the probabilities of short-range NOESY contacts in two ways:|
A) Experimental Probabilities: We used structures deposited at the PACSY database and filter them by the use of the MolProbility method. These structures are used for calculating the probabilities.
B) Theoretical Probabilities: In addition we used the TINKER molecular modeling package for exploring the potential surface of all the possible dipeptides. Among the structures generated in the simulations (217,402,896 conformations), we used the ones that are marked as local minima (22,010,359 conformations) of the amber99sb potential function and calculate the NOESY probabilities. The 22 millions used conformations could be downloaded in PDB format (11.7 GB).
Here, you can browse the probabilities for every two amino acids. The sequential distance between the amino acids could be 0 (intra-residue probabilities) up to 4 (probabilities between residues i and i±4). The default distance for observing NOESY contacts is set to be 5.5 Å.
Experimental NOESY Contacts Probabilities-PACSY:
A statistical analyses on these probabilities is conducted to generate the average and std. of the number of expected short-range NOESY contacts. This link shows the outcomes of this analysis.|
In addition, a similar analysis on the NMR Restraints Grid resulted on the average and std of the medium and long-range NOESY contacts. The results of this study are shown here.
For any question or concern please contact Hesam Dashti (firstname.lastname@example.org)