The second technique (TNR [ 77]) attempted to identify all associations (strictly association rules [ 123]) with strong statistical support, which we next filtered for those that predict p65 binding (see Methods and Additional file 1: Methods).
The artificial amino acid sequences are then submitted to NetMHC, configured to predict all 55 possible MHC alleles within the software (version 3.0), and only the predicted strongly binding peptides are filtered for further processing.
Starting from commercially available compounds, core fragments were extracted, filtered for pharmacophoric properties compatible with hinge-region binding, and docked into a panel of protein kinases.
In brief, 1 kb of sequence from each binding site is extracted and filtered for conserved sequences.
All fragments were docked into the ATP binding pocket, and each docking orientation was filtered for steric fit.
Nineteen genes associated with the growth hormone system (gh, igf, their receptors and binding proteins) were identified in the transcriptome and filtered for redundancy as previously described.
The output structures with the lowest binding energies were considered and the docked poses were filtered for catalytically productive conformations.
Out of the 64,000 compounds in the filtered set, binding modes for 5836 compounds were generated.
Therefore, proteomic profiles of all tissues can serve as a filter for TF-binding predictions based on DNA motifs or ChIP-seq profiles in common cell lines.
As an alternative to gain/loss patterns, ReXSpecies 2.0 supports the calculation of branch length scores as proposed by [ 37] for each transcription factor binding site prediction (as well as for gain/loss patterns), and to use these scores for ranking and filtering transcription factor binding site predictions.
