List of protein structure prediction software

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Please improve this article if you can. (August 2007)

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.

Contents

[edit] 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

[edit] 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

[edit] 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

[edit] 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

[edit] 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