Desktop and Web-based Gesamt Software for Fast and Accurate Structural Queries in the PDB

New software for fast screening of the Protein Data Bank in 3 dimensions is presented. The software represents a multi-threaded version of the Gesamt algorithm, described in a separate publication. The software is implemented as a Qt-powered desktop application Qt Gesamt, dedicated "Structural Alignment" task in the new CCP4 web-application " jsCoFE " (http://ccp4serv6.rcharwell. ac.uk/ jsCoFE /), as well as a Restful API for performing remote PDB searches from ordinary PC connected to the internet. The software takes advantage of multi-core architectures, typical for all modern computational platforms, for making fast structural searches in the PDB as well as pairwise and multiple alignments of protein structures in 3d. A combination of parallelization and data reduction techniques made it possible to perform structural queries on modern laptops with speeds that were previously obtainable only from specialized web-servers. A detail performance analysis of QtGesamt is given. QtGesamt and the corresponding Restful API are available for download from http://ccp4serv7.rc-harwell.ac.uk/ Gesamt. Keywords: Structure alignment; Structure superposition; Homology studies