We addressed the site homology for RAAs without violating the positional homology inferred for the structural aligned regions.
For a given target sequence, FINDSITE identifies ligand-bound template structures from a set of distantly homologous proteins recognized by the PROSPECTOR_3 threading approach and superposes them onto the target's structure using the TM-align structural alignment algorithm.
The TM-align structural alignment results revealed that, the top five PDB hits were 4nl6A, 1qonA, 2c3mB, 2fj0A and 1n35A and its TM scores were 0.843, 0.442, 0.432, 0.426 and 0.426 respectively.
The method was evaluated by performing an all-to-all comparison on two separate sets of ligand-binding sites, comprising 47 protein-FAD (Flavin-Adenine Dinucleotide) and 64 protein-NAD (Nicotinamide-Adenine Dinucleotide) complexes, and comparing the results with those of an existing sequence-based structural alignment tool (TM-Align).
For this, we compute structural alignments with TM-align and PPM and add them to the models under investigation.
A structural alignment algorithm, TM-align (33), was effective in identification of highly similar local structural matches (TM-score > 0.50) between targets and their corresponding homologues in Mtb.
Results: We analyze the self-consistency of seven widely-used structural alignment methods (SAP, TM-align, Fr-TM-align, MAMMOTH, DALI, CE and FATCAT) on a diverse, non-redundant set of 1863 domains from the SCOP database and demonstrate that even for relatively similar proteins the degree of inconsistency of the alignments on a residue level is high (30%).
In Prefab, the reference alignment is defined as the portions of alignments consistently aligned by two structural aligners: CE (Shindyalov and Bourne, 1998) and DALI (Holm and Sander, 1995).
We aligned the PRDs based on a published structural alignment [ 15], and aligned the peptide PWMs based on both the general PxxP pattern and some published alignments [ 15, 56].
The two family alignments were aligned using a structural alignment of the two protein structures.
