This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, and secondary structure prediction.

Homology modeling

NAME Method Description Link
MODELLER Satisfaction of spatial restraints Standalone program
in Python
SWISS-MODEL Local similarity/fragment assembly Automated webserver
(based on ProModII)
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

Threading/fold recognition

NAME Method Description Link
3D-PSSM 3D-1D sequence profiling Webserver server
Superfamily Hidden Markov modeling Webserver/standalone main page
PSI-BLAST Iterative sequence alignment for fold identification Webserver main page
Bioingbu Evolutionary information recognition Webserver server
PSIPRED/GenTHREADER Sequence profiling Webserver main page
LOOPP Multiple methods Webserver server

Ab initio structure prediction

NAME Method Description Link
ROSETTA/ROBETTA Fragment assembly without template Webserver server
Rosetta@Home Distributed-computing implementation of Rosetta algorithm Downloadable program main page
CABS Reduced modeling tool Downloadable program download

Secondary structure prediction

NAME Method Description Link
GOR Information theory/Bayesian inference Many implementations Basic GOR
Jpred Neural network assignment Webserver server
PredictProtein Profile-based neural network Webserver server
Meta-PP Consensus prediction of other servers Webserver main page
PREDATOR Knowledge-based database comparison Webserver server

Jpred compares the sequence of the query and the sequences found in the databases. Jpred uses a computer algorithm to allow for gaps, which represent insertions and deletions. This program identifies proteins that are homologous to the query sequence. Jpred also identifies if any homologous proteins have determined 3D structures.