LinkerDB

[…] atabase has expanded tremendously during the last decade, no further updates or improvements were made to the LINKER website since it was created, and it is no longer accessible.The web-based program LinkerDB (http://www.ibi.vu.nl/programs/linkerdbwww/) also provides a database containing linker sequences with various confirmations and a search engine. The search algorithm accepts several query ty […]

[…] the assembled structures; finally we docked them as rigid-bodies with ZDOCK [], and scored the docking poses with pyDock. Docking poses were further rescored with distance restraints derived from the linker database, according to linker sequence length (pyDockTET method). In order to evaluate the success of our predictions, we have defined an acceptable docking pose as one where the RMSD of one of […]