Protein Threading Software
- HHpred is a popular threading server which runs HHsearch, a widely used software for remote homology detection based on pairwise comparison of hidden Markov models.
- RAPTOR (software) is an integer programming based protein threading software. It has been replaced by a new protein threading program RaptorX / software for protein modeling and analysis, which employs probabilistic graphical models and statistical inference to both single template and multi-template based protein threading. RaptorX significantly outperforms RAPTOR and is especially good at aligning proteins with sparse sequence profile. The RaptorX server is free to public at RaptorX.
- Phyre is a popular threading server combining HHsearch with ab initio and multiple-template modelling.
- MUSTER is a standard threading algorithm based on dynamic programming and sequence profile-profile alignment. It also combines multiple structural resources to assist the sequence profile alignment.
- SPARKS X is a probabilistic-based sequence-to-structure matching between predicted one-dimensional structural properties of query and corresponding native properties of templates.
- BioShell is a threading algorithm using optimized profile-to-profile dynamic programming algorithm combined with predicted secondary structure.
Read more about this topic: Threading (protein Sequence)
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