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.
Geno3D is webserver for producing homology models by satisfaction of spatial restraints using methodology derived from NMR data processing. webserver
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 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.
Homology modeling
| Name | Method | Description | Link |
|---|---|---|---|
| 3D-JIGSAW | Fragment assembly | Automated webserver | server |
| RaptorX | remote homology detection, protein 3D modeling, binding site prediction | Automated webserver and Downloadable program | server and download |
| Biskit | wraps external programs into automated workflow | BLAST search, T-Coffee alignment, and MODELLER construction | project site |
| CABS | Reduced modeling tool | Downloadable program | download |
| CPHModel | Fragment assembly | Automated webserver | server |
| EasyModeller | GUI to MODELLER | Standalone windows executable | download |
| ESyPred3D | Template detection, alignment, 3D modeling | Automated webserver | server |
| FoldX | Energy calculations and protein design | Downloadable program | download |
| GeneSilico | Consensus template search/fragment assembly | Webserver | server |
| Geno3D | Satisfaction of spatial restraints | Automated webserver | server |
| HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | server download article |
| LIBRA I | LIght Balance for Remote Analogous proteins, ver. I | Webserver | server |
| LOMETS | Local Meta threading server | Meta-server combining 9 different programs | Server |
| MODELLER | Satisfaction of spatial restraints | Standalone program mainly in Fortran and Python | download Server |
| Phyre and Phyre2 | Remote template detection, alignment, 3D modeling, multi-templates, ab initio | Webserver with job manager, automatically updated fold library, genome searching and other facilities | server |
| Prime | Physics-based energy function | Graphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction | Download |
| Protinfo CM | Comparative modelling of protein structure using minimum perturbation and loop building | Web server | server |
| ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
| BHAGEERATH-H | Combination of ab initio folding and homology methods | Protein tertiary structure predictions | server |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: BLAST search, CABS modeling, 3D threading, Psi-Pred secondary structure prediction | Home page |
| STRUCTUROPEDIA | WebInterface to MODELLER | Homology modeling of proteins in monomeric or multimeric forms alone and in complex with peptides and DNA as well as introduction of mutations and post-translational modifications (PTMs) into protein structures | server |
| SWISS-MODEL | Local similarity/fragment assembly | Automated webserver (based on ProModII) | server |
| TIP-STRUCTFAST | Automated Comparative Modeling | Webserver and knowledgebase | server |
| WHAT IF | Position specific rotamers | Standalone program and webinterface | Home page Webinterface |
| Yasara | Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments | Graphical interface or text mode (clusters) | Home page CASP8 results |
Threading/fold recognition
| Name | Method | Description | Link |
|---|---|---|---|
| RaptorX | Remote template detection, single-template and multi-template threading, totally different from and much better than the old program RAPTOR designed by the same group | Webserver with job manager, automatically updated fold library | download server |
| 3D-PSSM | 3D-1D sequence profiling (replaced by Phyre) | Webserver | server |
| Bioingbu | Evolutionary information recognition | Webserver | server |
| FALCON@home | Single-template and multi-template threading, a high-throughput server based on volunteer computing | Webserver with job manager | article server |
| HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | server download article |
| NovaFold | Combination of threading and ab initio folding | Commercial protein structure prediction application | Home page |
| I-TASSER | Combination of ab initio folding and threading methods | Structural and function predictions | server |
| LOOPP | Multiple methods | Webserver | server |
| mGenTHREADER/GenTHREADER | Sequence profile and predicted secondary structure | Webserver | main page |
| MUSTER | profile-profile alignment | Webserver | server |
| Phyre and Phyre2 | Remote template detection, alignment, 3D modeling, multi-templates, ab initio | Webserver with job manager, automatically updated fold library, genome searching and other facilities | server |
| RAPTOR | Integer programming based fold recognition | Free demo | download articles |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: 3D threading and flexible 3d threading | Home page |
| SUPERFAMILY | Hidden Markov modeling | Webserver/standalone | main page |
| SPARKS-X | 3D structure modeling by Fold recognition according to Sequence profiles and structural profiles | Webserver | Server |
| BBSP - Building Blocks Structure Predictor | Hybrid template-based | Free application plus database | main page |
Ab initio structure prediction
| Name | Method | Description | Link |
|---|---|---|---|
| EVfold | Evolutionary couplings calculated from correlated mutations in a protein family, used to predict 3D structure from sequences alone and to predict functional residues from coupling strengths. Predicts both globular and transmembrane proteins. | Webserver | Server |
| FALCON | A position-specific hidden Markov model to predict protein structure by iteratively refining the distributions of dihedral angles | Webserver | article server |
| QUARK | Monte Carlo fragment assembly | On-line server for protein modeling (best for ab initio folding in CASP9) | Server |
| NovaFold | Combination of threading and ab initio folding | Commercial protein structure prediction application | Home page |
| I-TASSER | Threading fragment structure reassembly | On-line server for protein modeling | Server |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Interactive webserver and standalone program including: CABS ab initio modeling | Home page |
| ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
| Rosetta@home | Distributed-computing implementation of Rosetta algorithm | Downloadable program | main page |
| CABS | Reduced modeling tool | Downloadable program | download |
| CABS-FOLD | Server for de novo modeling, can also use alternative templates (consensus modeling). | Webserver | server |
| Bhageerath | A computational protocol for modeling and predicting protein structures at the atomic level. | Webserver | Server |
| Abalone | Molecular Dynamics folding | Program | Example |
| PEP-FOLD | De novo approach, based on a HMM structural alphabet | On-line server for peptide structure prediction | Server |
Secondary structure prediction
Detailed list of programs can be found at List of protein secondary structure prediction programs
Transmembrane helix prediction
| Name | Method | Description | Link |
|---|---|---|---|
| HMMTOP | Hidden Markov Model | Webserver/standalone | main page |
| MEMSAT | Neural networks and SVMs | Webserver/standalone | main page |
| PHDhtm in PredictProtein | Multiple alignment-based neural network system | Webserver/standalone | server |
| Phobius | Homology supported predictions | Webserver/standalone | main page |
| TMHMM | Hidden Markov Model | Webserver/standalone | main page |
| CCTOP | Consensus/Hidden Markov Model | Webserver/standalone | main page |
| SVMTop2 | Support Vector Machines | Webserver | main page |
Signal peptide prediction
| Name | Method | Description | Link |
|---|---|---|---|
| SignalP | artificial neural networks and hidden Markov models | Webserver/standalone | server |
See also
- List of protein secondary structure prediction programs
- Comparison of nucleic acid simulation software
- List of software for molecular mechanics modeling
- Molecular design software
- Protein design
References
- ↑ "Probing the protein space for extending the detection of weak homology folds". Journal of Theoretical Biology. 320: 152–58. doi:10.1016/j.jtbi.2012.12.005.