The procedure of restoring missing coordinate of the crystal loop is described.
Gene OA1 and KCNJ18 (OMIM: 613236) were also missing coordinate information.
A "manual scoring" analysis was also performed to identify the missing coordinate from probes having two positive pools.
Furthermore, in the geographical analyses of holdings we excluded 73 (2,3%) of the active pig holdings and 3309 (11%) of the active cattle holdings due to missing coordinate data, and thus our results underestimate the true number of holdings within the 3 km and 10 km radius and the number of movements at certain distances and between counties.
For cases with missing coordinates, the structures were rebuilt using CORINA [58].
In addition to various modules from the standard library, it uses the indigo cheminformatics library and its accompanying Python API [10, 11], which it relies on for parsing of molfile and SMILES input, addition or removal of hydrogen atoms, and the calculation of missing coordinates.
One limitation of methods based on machine learning is that they are prone to over-optimization when developed on data sets as small as the Database of Protein Disorder (DisProt) or as specialized as missing coordinates from the Protein Data Bank (PDB).
Interestingly, this is consistent with predictions resulting from profiling the intrinsic disorder propensity of PTP-SL by two distinct methods (FIG. 8A, B), based either on scores derived from missing coordinates in high resolution protein crystals [23], or pairwise energy estimates from the amino acid composition [24].
First, we calculated the arithmetic average over the raw output of four disorder prediction methods: DISOPRED2 (Support Vector Machine based prediction of missing coordinates in X-ray structures), IUPred (prediction of unstructured regions based on pairwise statistical potential), NORSnet (prediction of unstructured loops) and Ucon (specific contact based prediction method).
2. Run MODELLER to generate 500 model candidates for residues with missing coordinates (missing loop region).
Part of the future work will be better handling of residue modification and missing coordinates.
