AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands

Abstract

Understanding the mechanism of action of a protein or designing better ligands for it often requires access to a bound (holo) and an unbound (apo) state of the protein. Resources for the quick and easy retrieval of such conformations are severely limited. Apo-Holo Juxtaposition (AHoJ) is a web application for retrieving apo-holo structure pairs for user-defined ligands. Given a query structure and one or more defined ligands, it retrieves all other structures of the same protein that feature the same binding sites(s), aligns them, and examines the superimposed binding sites to determine whether each structure is apo or holo, in reference to the query. The resulting superimposed datasets of apo-holo pairs can be visualized and downloaded for further analysis. AHoJ accepts multiple input queries, allowing the creation of customized apo-holo datasets. To demonstrate AHoJs functionality, we present a newly constructed dataset of apo-holo pairs featuring 13 ion ligands, by complimenting an existing database of biologically relevant holo interactions (BioLiP). Availability and ImplementationFreely available for non-commercial use at http://apoholo.cz. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/496878v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@1e34d98org.highwire.dtl.DTLVardef@1fb3d47org.highwire.dtl.DTLVardef@1742435org.highwire.dtl.DTLVardef@1f54dc3_HPS_FORMAT_FIGEXP M_FIG C_FIG