From DrugPedia: A Wikipedia for Drug discovery
The 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.
[edit] Homology modeling
Table I
Homology modeling softwares
| Name
| Method
| Description
| Link
|
| 3D-JIGSAW
| Fragment assembly | Automated webserver | server
|
| CABS
| Reduced modeling tool | Downloadable program | download
|
| CPHModel
| Fragment assembly | Automated webserver | server
|
| ESyPred3D
| Template detection, alignment, 3D modeling | Automated webserver | server
|
| 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
|
| MODELLER
| Satisfaction of spatial restraints | Standalone program in Python | download
|
| ROSETTA
| Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | 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 | Webserver | server
|
[edit] Threading/fold recognition
Table II
Threading/fold recognition softwares
| 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
|
[edit] Ab initio structure prediction
Table III
Ab initio structure prediction softwares
| 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
|
[edit] Secondary structure prediction
Table IV
Secondary structure prediction softwares
| Name
| Method
| Description
| Link
|
| APSSP2
| multiple alignment, neural network and MBR techniques | webserver | server
|
| 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
|
[edit] Transmembrane helix and signal peptide prediction
Table V
Transmembrane helix and signal peptide prediction softwares
| 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
|
