Software
I-TASSER is the best server for protein structure prediction according to the 2006-2010 CASP experiments (CASP7, CASP8 and CASP9). The standalone I-TASSER package is freely available for download.
RaptorX excels at aligning hard targets according to the 2010 CASP9 experiments. RaptorX generates the significantly better alignments for the hardest 50 CASP9 template-based modeling targets than other servers including those using consensus and refinement methods. The RaptorX server is available at server
MODELLER is a popular software tool for producing homology models using methodology derived from NMR spectroscopy data processing.
SwissModel provides an automated web server for basic homology modeling.
HHpred, bioinfo.pl and Robetta widely used servers for protein structure prediction. HHsearch is a free software package for protein threading and remote homology detection.
SPARKSx is one of the top performing servers in the CASP focused on the remote fold recognition.
PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences, based on a HMM structural alphabet.
Phyre and Phyre2 are amongst the top performing servers in the CASP international blind trials of structure prediction in homology modelling and remote fold recognition, and are designed with an emphasis on ease of use for non-experts.
RAPTOR (software) is a protein threading software that is based on integer programming. The basic algorithm for threading is described in Bowie (1991) and is fairly straightforward to implement.
QUARK is an on-line server suitable for ab initio protein structure modeling.
Abalone is a Molecular Dynamics program for folding simulations with explicit or implicit water models.
TIP is a knowledgebase of STRUCTFAST models and precomputed similarity relationships between sequences, structures, and binding sites. Several distributed computing projects concerning protein structure prediction have also been implemented, such as the Folding@home, Rosetta@home, Human Proteome Folding Project, Predictor@home, and TANPAKU.
The Foldit program seeks to investigate the pattern-recognition and puzzle-solving abilities inherent to the human mind in order to create more successful computer protein structure prediction software.
Computational approaches provide a fast alternative route to antibody structure prediction. Recently developed antibody FV region high resolution structure prediction algorithms, like RosettaAntibody, have been shown to generate high resolution homology models which have been used for successful docking.
Reviews of software for structure prediction can be found at.
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