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Table 4 Eight predictions of which their holo structures have been identified through a homologous searching process using MAMMOTH

From: Prediction of calcium-binding sites by combining loop-modeling with machine learning

Protein name PDB ID Loop   FEATURE score Holo structure Alignement
   Start End Sequence CaDis(Å) Gap Loop SCOP ID Start End CaDis(Å) PRA RMSD PID
CONCANAVALIN A 1APN_A 15 23 TD IGD PSYP 2.40 9.15 58.19 d1vald_ 15 23 1.94 99 1.61 96
C-REACTIVE PROTEIN 1LJ7_H 142 149 FGGNFE GS 1.94 -18.56 55.46 d1gnhc_ 142 149 1.99 100 0.74 100
SOLUBLE INORGANIC PYROPHOSPHATASE 1IPW_A 97 101 DE AGE 4.67 47.13 53.38 d1i6ta_ 97 101 2.19 99 1.49 91
BE TA-KETOACYL REDUCTASE 1I01_C 140 149 VGTMGNGGQA 2.25 7.93 56.74 d1q7bd_ 140 149 2.41 96 1.96 89
OBELIN 1SL9_A 122 128 FD KD GSG 1.96 -1.98 50.80 d1sl7a_ 122 128 2.43 98 2.89 89
DEOXYRIBONUCLEASE I 2DNJ_A 99 107 D GCE SCGND 2.07 42.69 72.61 d3dnia_ 99 107 2.57 100 0.87 98
STAPHYLOCOCCAL NUCLEASE 1SNQ_A 44 51 TKHGKKGV 4.17 45.69 66.14 d1nuca_ 44 51 4.88 98 1.70 92
SOLUBLE INORGANIC PYROPHOSPHATASE 1FAJ_A 145 149 E KGKW 3.35 39.95 51.60 d1i40a_ 146 149 5.37 99 1.59 87
  1. Column 2 lists protein name that is PDB code followed by the chain identifier. We build structures for gaps of which 3D structures are not present in the original PDB files. Information of these structures, referred as "loop", is given in column 2-5. Column 5 lists the distances from the predicted sites to the rebuilt loops (CaDis). Column 6 and 7 list FEATURE scores at the predicted sites in the structures where loop structures are missing (Gap) and in the rebuilt loop structures (Loop). Ligands observed experimentally are listed in column 8 and the ligand IDs are from PDB. Column 9 shows the SCOP ID of the holo structures. Information of aligned counterparts for the binding loops is listed in column 10-12. Column 12 lists the distances from the calcium ions to the aligned loop counterparts (CaDis). The percentage of residues aligned (PRA), the RMSD of the aligned regions, and the percentage of identical residues (PID) are shown in column 13-15.