MADOKA, a webserver features on searching similar protein structures by aligning input structure with the whole PDB library implemented by MADOKA, an algorithm for matching protein structures by two phases.
Usage Notes: The upload protein structure file should be in PDB format. Most tasks will be finished in 15-60 minutes. Results include a list contains up to 50 most similar aligned structures with your input structure that the ratio of length between the long structure and the short structure between a result pair is less than 1.5, additionally, there will be alignment results and superposed Ca-traces for the template structure in output files. Here is a pre-calculated example to display the search results: 1A1O_A If you have multiple structures to run on the web server, we advise you to upload the next structure after the previous one have finished all steps of searching and aligning, it's much faster than upload all structures at once.
For questions about MADOKA server, please email Lei Deng for assistance.