Overview of SRPmotif using Isoleucyl-tRNA synthetase-Mupirocin complex as example. (A) Identify polypharmacological candidates with similar discontinuous binding segments by rapidly searching protein structure databases using 3D-BLAST. The proteins with 75% similar binding segments are considered as the candidates of the polypharmacological candidates. (B) These candidates with significantly similar interfaces (RMSD ≤ 2.0Å and average aligned ratio ≥ 0.85) are considered as polypharmacological proteins. (C) The polypharmacological proteins are used to recognize the conserved segments (pharma-motifs) which can be transformed into 1D sequence patterns based on the multiple structural alignments. These spatially discontinuous pharma-motifs are formed a pharma-interface for these polypharmacological proteins.
Chiu et al. BMC Genomics 2012 13(Suppl 7):S21 doi:10.1186/1471-2164-13-S7-S21