List of 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.

Software highlight

I-TASSER is the best server for protein structure prediction according to the 2006-2012 CASP experiments (CASP7, CASP8, CASP9, CASP10, and CASP11). 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.

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 by satisfaction of spatial restraints using methodology derived from NMR spectroscopy data processing. The ModWeb comparative protein structure modeling web-server uses primarily MODELLER for automatic comparative modeling.

SWISS-MODEL provides an automated web server for protein structure homology modeling.

bioinfo.pl and Robetta widely used servers for protein structure prediction.

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 algorithm developed 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.

Princeton_TIGRESS (server) is a protein structure refinement server whose underlying method was ranked in 5th place in blind predictions during CASP10 <http://predictioncenter.org/casp10/doc/presentations/ranking_CASP10_refinement_DJ.pdf>. It uses monte carlo and molecular dynamics based sampling techniques and support vector machines for selection. It can consistently increase the model accuracy of many top 3-D structure prediction servers' predictions, increasing the potential usability of a predicted structure in a biological application.

CABS-FOLD is a server that provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling).

Bhageerath is another Ab-initio modelling server.

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.

BBSP (Building Blocks Structure Predictor) is a program that makes use of Hybrid template-based approaches, which associate fragment conformations for the sequence and detect distant fold similarities based on the fragment similarities <http://rsif.royalsocietypublishing.org/content/11/95/20131147>. Also, such program is assisted by a secondary structure prediction algorithm named HCAM, which is mainly based on hydropathy profile analysis and is included in the BBSP tools suite.^[1]

Computational approaches provide a fast alternative route to antibody structure prediction. Recently developed antibody F_V region high resolution structure prediction algorithms, like RosettaAntibody, have been shown to generate high resolution homology models which have been used for successful docking.

Homology modeling

Threading/fold recognition

Ab initio structure prediction

Secondary structure prediction

Detailed list of programs can be found at List of protein secondary structure prediction programs

Transmembrane helix prediction

Signal peptide prediction

See also

• List of protein secondary structure prediction programs
• List of nucleic acid simulation software
• List of software for molecular mechanics modeling
• Molecular design software
• Protein design

References