- Sphinx is a protein loop modelling algorithm that combines knowledge-based and ab initio approaches.
- Given a protein structure, location of the loop to be modelled and the sequence of that loop, it searches a database of fragments for sections of other proteins that are shorter than the target loop, but that may have some structural similarity. By using ab initio techniques, the loop conformations can be made to be the correct length.
- Once a set of conformations has been produced, a fast statistical potential is used to cull the set to only 500 structures, which are then scored using SOAP-Loop (Dong et al., 2013) to produce a ranking.
- An example of the output produced by Sphinx can be seen here.
If you have not already done so, we recommend first running FREAD, a knowledge-based algorithm which can also produce accurate predictions but requires less computation time.
For a full description of the pipeline, or if you use this software, please refer to: Marks, C. et al. Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics. (2017)