Protein structure prediction software

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.

I-TASSER is the best server for protein structure prediction according to the 2006–2016 CASP experiments (CASP7, CASP8, CASP9, CASP10, CASP11, and CASP12). The standalone I-TASSER package is freely available for download.

HHpred was the leading server for template-based protein structure prediction in the 2010 CASP9 experiment. It has a median response time of a few minutes instead of days like other top-performing servers. 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.

DNASTAR's NovaFold is protein structure prediction software that is based on I-TASSER. NovaFold utilizes the I-TASSER algorithms that combine threading and ab initio folding technologies to build accurate, full 3D atomic models of proteins with previously unknown structures. NovaFold is available locally and as cloud-based software.

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