List of protein structure prediction software

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.

Contents 1 Homology modeling 2 Threading/fold recognition 3 Ab initio structure prediction 4 Secondary structure prediction 5 Transmembrane helix and signal peptide prediction

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

Threading/fold recognition

Table II:

Homology modeling 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

Ab initio structure prediction

Table III:

Homology modeling 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

Secondary structure prediction

Table IV:

Homology modeling softwares

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