PMC:1867812 / 19959-20758 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1867812","sourcedb":"PMC","sourceid":"1867812","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1867812","text":"When generating contact maps, we consider the Euclidean distances between α-carbons (Cα) of each amino acid. Two α-carbons are considered to be in contact if their distance is within 8.5 Å. Thus, for a protein of N residues, its contact map is an N × N binary matrix, where the cell at (i, j) is 1 if the ith and jth α-carbons are in contact, 0 otherwise. Since contact maps are symmetric across the diagonal, we only consider the bits below the diagonal. Furthermore, we also ignore the pairs of Cα atoms whose distance in the primary sequence is ≤ 2, as they are sure to be in contact. This step transforms the two BBA5 trajectories into two series of contact maps, with each contact map of size 23 × 23. By the same token, the 5 GSGS trajectories are transformed into 5 sequences of contact maps.","tracks":[]}