Similar protocols

Pipeline publication

[…] on (P), Recall (R), and Performance (F) statistics were computed for sets of EC contacts or expanded lists of Residue Pair Contacts (RPCs) resulting from the EC-NMR protocol as: Eqn. 1P=TP/(TP+FP) Eqn. 2R=TP/(TP+FN) Eqn. 3F=(2×R×P)/(R+P), In this analysis a TP contact is defined for residue pair (i,j) if any atom of residue i is ≤ 5 Å apart from any atom of residue j in the reference structure. An EC (or RPC) for which a contact is not indicated in the reference structure is a FP. A contact in the reference structure which is not included in the EC (or RPC) list is a FN., When X-ray crystal structures were used as the reference structure, hydrogens were added using the Reduce program of the Molprobity software package. When NMR ensembles were used as the reference structure, a TP was defined if this criterion was satisfied for at least 60% of the conformers in the NMR ensemble. The Precision statistic is the fraction of TPs in all the predicted contacts. Recall (R) is the fraction of TPs identified compared to all the contacts observed in the reference structure. These P, R, and F statistics assume that the experimental X-ray crystal or NMR structure is the “ground truth”, and the EC or RPC contacts are the “prediction”. They differ from those used in assessing NMR models against NMR NOESY peak list data (NMR RPF), in which the model is taken as the “prediction” and the NOESY data is the “ground truth”., Backbone (defined as N, Cα, C’, and O atoms) and all-heavy-atom (N, C, O, S) Root Mean Square Deviations (RMSDs) were computed using the fit command, for specified residue ranges, as implemented in the PyMol software., We thank all of the members of the Northeast Structural Genomics Consortium who generated and archived NMR data used in this work, particularly scientists in the laboratories of C. Arrowsmith, M. Kennedy, G.T. Montelione, T. Szyperski, and J. Prestegard. We also thank J. Aramini, G. Liu, G.V.T. Swapna, H. Valafar, M. Nilges, and F. Xu for helpful discussions. This work was supported by grants from the National Institutes of Health: grant 1R01-GM106303 to C.S. & D.M. and Protein Structure Initiative grant U54-GM094597 to G.T.M., Author Contributions Y.T., Y.J.H., T.H., C.S., D.S.M. and G.T.M. designed the research. Y.J.H. wrote ASDP program code. Y.T., Y.J.H. T.H., and D. […]

Pipeline specifications

Software tools MolProbity, RPF, PyMOL