Binding sites with >5 residues were outputted, and 54,936 binding sites were extracted, which could bind with 12,138 ligands.
The 978 ATP-binding binding sites were extracted from the sc-PDB database [39] and feature a total of 433 unique proteins among which 110 are protein kinases.
Sequences of axis protein binding sites were extracted from the genome using Python scripts (Supplementary file 2).
The fungal LSU rDNAs containing the binding sites of both primers were kept and the corresponding segments between the two binding sites were extracted.
Genomic sequence of miRNA cluster and the predicted transcription factor binding sites were extracted from the " Cis-element clusters within BlastZ Aligments" option at the GenomeTraFac [ 44].
Interaction data used to build the human interaction matrix and to classify RBP binding sites were extracted from the AURA 2 database (/ http://aura.science.unitn.it/download/).it/download/
Sequence windows of length 21, the average length of CaM binding sites, were extracted from the protein sequences to create positive and negative examples.
In a first step, alternative conformations of a given binding site are extracted from an arbitrary selection of protein structures, e.g. the current version of the Protein Data Base (PDB).
The coordinates of the binding site were extracted using the co-crystallized ligand, Ibuprofen.
In brief, 1 kb of sequence from each binding site is extracted and filtered for conserved sequences.
