PBBD - Protein Building Blocks Database: Detection of structural, functional, and evolutionary features of unclassified protein by mining a collection of basic PDB stand alone units (closed loops, αβ-barrels, helix-loop-helix, greek keys, coiled coils, βαβ-motifs, β-strands, EF hands, Zinc fingers, intrinsecally disordered regions, etc.) taken from several domain superfolds (Rossman folds, TIM barrels, αβ-sandwiches, αβ open sheets, etc.). At present the PBBD includes up to 7960 structures, ranging from 3 to 145 mers - read more...
ISHN - Indiscernible Sequence Homology Network. We have retrieved data from the PBBD to construct a network of subdomain-size structural analogs sharing less than 20% aminoacidic identity for remote homology detection. The ISHN and other supplementary networks are available in Tools section. We are aiming at expanding the ISHN by detecting the emergenze of 'sub-domain-size discrete islands' that make sense from an evolutionary perspective read more...
LUCA and SUCA - Last-/Structural Universal Common Ancestor. Exploration of evolutionary relationships within the protein universe at sub-domain-size resolution, in order to detect ancient signals (i. e. elementary functions and elementary structures) that belong to the last universal common ancestors (LUCA) and the structural universal common ancestor (SUCA).
ARRD - 'Allosteric Reverters' rational design. Computational design of allosteric modulators which restore wild-type functions of protein mutants.
EBPI - Evolutionary-Based Peptide Inhibitors. Evolutionary-based rational design of peptide inhibitors which bind at the protein sub-units interface level.
PSPR - Protein Structure Prediction Refiner. A method that refines protein structure prediction outcomes achieved by artificial intelligence algorithms.