Profrager Web Server: Fragment Libraries Generation for Protein Structure Prediction

摘要

This paper describes Profrager, a new flexible web server for generation of protein fragment libraries. These libraries have widespread use amongst modern protein structure prediction methods. Profrager offers several options for generating customized libraries, e.g., the users can choose between three options of structural databases to generate the libraries and can also define the number of fragments per position and the fragments lengths. The selection of fragments can be guided by three scoring strategies: (i) use only sequence similarity to the target sequence; (ii) use a weighted sum of the sequence similarity score and a secondary structure score; (iii) use a Pareto Efficiency strategy with the two scores. The software outputs useful statistics about the fragments in addition to files fully compatible with the GAPF and Rosetta protein structure prediction programs. Profrager is available at http://www.lncc.br/sinapad/Profrager/as a web service.