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This article’s use of external links may not follow Wikipedia’s policies or guidelines. Please improve this article by removing excessive or inappropriate external links, and converting useful links where appropriate into footnote references. This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction. The protein structure prediction pdf I-TASSER package is freely available for download.


HHpred is often used for remote homology detection and homology-based function prediction. It runs with the free, open-source software package HH-suite for fast sequence searching, protein threading and remote homology detection. RaptorX excels at aligning hard targets according to the 2010 CASP9 experiments. MODELLER is a popular software tool for producing homology models by satisfaction of spatial restraints using methodology derived from NMR spectroscopy data processing.

Robetta is a ten-step pipeline of multiple bioinformatics tools, notably the Rosetta software suite of algorithms for computational modeling and analysis of protein structures. Rosetta development began in the laboratory of Dr. Baker as a structure prediction tool but since then has been adapted to solve common computational macromolecular problems.

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