Protein Structure Prediction Software
See also:
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.
Homology modeling
| Name |
Method |
Description |
Link |
| MODELLER |
Satisfaction of spatial restraints |
Standalone program in Python |
download |
| SWISS-MODEL |
Local similarity/fragment assembly |
Automated webserver (based on ProModII) |
server |
| HHpred |
Template detection, alignment, 3D modeling |
Interactive webserver with help facility |
server download article |
| ROSETTA |
Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction |
Webserver |
server |
| 3D-JIGSAW |
Fragment assembly |
Automated webserver |
server |
| Geno3D |
Satisfaction of spatial restraints |
Automated webserver |
server |
| CPHModel |
Fragment assembly |
Automated webserver |
server |
| GeneSilico |
Consensus template search/fragment assembly |
Webserver |
server |
| WHAT IF |
Position specific rotamers |
Webserver |
server |
| TIP-STRUCTFAST |
Automated Comparative Modeling |
Webserver and knowledgebase |
server |
| CABS |
Reduced modeling tool |
Downloadable program |
download |
| LIBRA I |
LIght Balance for Remote Analogous proteins, ver. I |
Webserver |
server |
Threading/fold recognition
| Name |
Method |
Description |
Link |
| PSI-BLAST |
Iterative sequence alignment for fold identification |
Webserver |
main page |
| HHpred |
Template detection, alignment, 3D modeling |
Interactive webserver with help facility |
server download article |
| 3D-PSSM |
3D-1D sequence profiling |
Webserver |
server |
| SUPERFAMILY |
Hidden Markov modeling |
Webserver/standalone |
main page |
| Bioingbu |
Evolutionary information recognition |
Webserver |
server |
| mGenTHREADER/GenTHREADER |
Sequence profile and predicted secondary structure |
Webserver |
main page |
| LOOPP |
Multiple methods |
Webserver |
server |
Ab initio structure prediction
| Name |
Method |
Description |
Link |
| 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 |
| Bhageerath |
A computational protocol for modeling and predicting protein structures at the atomic level. |
Webserver |
Server |
Secondary structure prediction
| Name |
Method |
Description |
Link |
| GOR |
Information theory/Bayesian inference |
Many implementations |
Basic GOR GOR V |
| Jpred |
Neural network assignment |
Webserver |
server |
| Meta-PP |
Consensus prediction of other servers |
Webserver |
main page |
| PREDATOR |
Knowledge-based database comparison |
Webserver |
server |
| PredictProtein |
Profile-based neural network |
Webserver |
server |
| PSIPRED |
two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST |
Webserver |
server |
| YASSPP |
Cascaded SVM-based predictor using PSI-BLAST profiles |
Webserver |
server |
Transmembrane helix and signal peptide prediction
| Name |
Method |
Description |
Link |
| HMMTOP |
Hidden Markov Model |
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 |
|
Webserver/standalone |
main page |
This article is licensed under the GNU Free Documentation License. It uses material from Wikipedia Encyclopedia article "Protein Structure Prediction Software"
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