Protein-Protein-Docking high-performance computers
Docking is a universal approach in bioinformatics to predict the structure of macromolecule complexes. It proceeds in a two-step fashion: first, a large number of putative complex geometries is generated (sampling). Those complexes are then ranked according to their biological plausibility (scoring).
So far, we have developed a web server that offers a powerful algorithm for the scoring step. In expansion of the server's capabilities, KONWIHR funding now allows us to integrate the 3D sampling step for protein complexes. We decided to adapt the FTDock software package whose sole current parallelization (CellDock) features a highly processor-specific code base. In contrast, we rely on the MPI framework to reduce the sampling time requirement by at least one magnitude of order and allow a higher throughput on our web server. Additionally, the communication with the HPC queuing system will be established.
- KONWIHR funding: two months during Multicore-Software-Initiative 2013
- Prof. Dr. Heinrich Sticht, Institut für Biochemie, Uni-Erlangen
- Martin Eberhardt, Institut für Biochemie, Uni-Erlangen