MDT prepares a raw frequency table, given information from MODELLER alignments and/or PDB files. More precisely, MDT uses a sample of sequences, structures, and/or alignments to construct a table N(a,b,c,…,d) for features a, b, c, …, d. The sample for generating the frequencies N is obtained depending on the type of features a, b, c, …, d. The sample can contain individual proteins, pairs of proteins, pairs of residues in proteins, pairs of aligned residues, pairs of aligned pairs of residues, chemical bonds, angles, dihedral angles, and pairs of tuples of atoms. Some features work with triple alignments, too. All the needed features a, b, c, …, d are calculated automatically from the sequences, alignments, and/or PDB files. The feature bins are defined by the user when each feature is created.
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