List of protein structure prediction software

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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.

Software highlight[edit]

I-TASSER is the best server for protein structure prediction according to the 2006-2012 CASP experiments (CASP7, CASP8, CASP9 and CASP10). The standalone I-TASSER package is freely available for download.

HHpred was the leading server for template-based protein structure prediction in the 2010 CASP9 experiment. It has a median response time of a few minutes instead of days like other top-performing servers. HHpred is often used for remote homology detection and homology-based function prediction. It runs with the free, open-source software package HH-suite for fast sequence searching, protein threading and remote homology detection.

RaptorX excels at aligning hard targets according to the 2010 CASP9 experiments. RaptorX generates the significantly better alignments for the hardest 50 CASP9 template-based modeling targets than other servers including those using consensus and refinement methods. The RaptorX server is available at server

MODELLER is a popular software tool for producing homology models by satisfaction of spatial restraints using methodology derived from NMR spectroscopy data processing. The ModWeb comparative protein structure modeling web-server uses primarily MODELLER for automatic comparative modeling.

SWISS-MODEL provides an automated web server for protein structure homology modeling.

bioinfo.pl and Robetta widely used servers for protein structure prediction.

SPARKSx is one of the top performing servers in the CASP focused on the remote fold recognition.

PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences, based on a HMM structural alphabet.

Phyre and Phyre2 are amongst the top performing servers in the CASP international blind trials of structure prediction in homology modelling and remote fold recognition, and are designed with an emphasis on ease of use for non-experts.

RAPTOR (software) is a protein threading software that is based on integer programming. The basic algorithm for threading is described in Bowie (1991) and is fairly straightforward to implement.

QUARK is an algorithm developed for ab initio protein structure modeling.

Abalone is a Molecular Dynamics program for folding simulations with explicit or implicit water models.

TIP is a knowledgebase of STRUCTFAST models and precomputed similarity relationships between sequences, structures, and binding sites. Several distributed computing projects concerning protein structure prediction have also been implemented, such as the Folding@home, Rosetta@home, Human Proteome Folding Project, Predictor@home, and TANPAKU.

Princeton_TIGRESS (server) is a protein structure refinement server whose underlying method was ranked in 5th place in blind predictions during CASP10 (http://predictioncenter.org/casp10/doc/presentations/ranking_CASP10_refinement_DJ.pdf). It uses monte carlo and molecular dynamics based sampling techniques and support vector machines for selection. It can consistently increase the model accuracy of many top 3-D structure prediction servers' predictions, increasing the potential usability of a predicted structure in a biological application.

CABS-FOLD is a server that provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling).

Bhageerath is another Ab-initio modelling server.

The Foldit program seeks to investigate the pattern-recognition and puzzle-solving abilities inherent to the human mind in order to create more successful computer protein structure prediction software.

Computational approaches provide a fast alternative route to antibody structure prediction. Recently developed antibody FV region high resolution structure prediction algorithms, like RosettaAntibody, have been shown to generate high resolution homology models which have been used for successful docking.

Homology modeling[edit]

Main article: Homology modeling
Name Method Description Link
3D-JIGSAW Fragment assembly Automated webserver server
RaptorX remote homology detection, protein 3D modeling, binding site prediction Automated webserver and Downloadable program server and download
Biskit wraps external programs into automated workflow BLAST search, T-Coffee alignment, and MODELLER construction project site
CABS Reduced modeling tool Downloadable program download
CPHModel Fragment assembly Automated webserver server
EasyModeller GUI to MODELLER Standalone windows executable download
ESyPred3D Template detection, alignment, 3D modeling Automated webserver server
FoldX Energy calculations and protein design Downloadable program download
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
LOMETS Local Meta threading server Meta-server combining 9 different programs Server

download

MODELLER Satisfaction of spatial restraints Standalone program mainly in Fortran and Python download Server
Phyre and Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio Webserver with job manager, automatically updated fold library, genome searching and other facilities server
Prime Physics-based energy function Graphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction Download
Protinfo CM Comparative modelling of protein structure using minimum perturbation and loop building Web server server
ROBETTA Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction Webserver server
BHAGEERATH-H Combination of ab initio folding and homology methods Protein tertiary structure predictions server
Selvita Protein Modeling Platform Package of tools for protein modeling Free demo, interactive webserver and standalone program including: BLAST search, CABS modeling, 3D threading, Psi-Pred secondary structure prediction Home page
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 Standalone program and webinterface Home page Webinterface
Yasara Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments Graphical interface or text mode (clusters) Home page CASP8 results

Threading/fold recognition[edit]

Main article: Protein threading
Name Method Description Link
RaptorX Remote template detection, single-template and multi-template threading, totally different from and much better than the old program RAPTOR designed by the same group Webserver with job manager, automatically updated fold library download
server
3D-PSSM 3D-1D sequence profiling (replaced by Phyre) Webserver server
Bioingbu Evolutionary information recognition Webserver server
HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility server download article
NovaFold Combination of threading and ab initio folding Commercial protein structure prediction application Home page
I-TASSER Combination of ab initio folding and threading methods Structural and function predictions server

download

LOOPP Multiple methods Webserver server
mGenTHREADER/GenTHREADER Sequence profile and predicted secondary structure Webserver main page
MUSTER profile-profile alignment Webserver server

download

Phyre and Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio Webserver with job manager, automatically updated fold library, genome searching and other facilities server
RAPTOR Integer programming based fold recognition Free demo download
articles
Selvita Protein Modeling Platform Package of tools for protein modeling Free demo, interactive webserver and standalone program including: 3D threading and flexible 3d threading Home page
SUPERFAMILY Hidden Markov modeling Webserver/standalone main page
SPARKS-X 3D structure modeling by Fold recognition according to Sequence profiles and structural profiles Webserver Server

Ab initio structure prediction[edit]

Name Method Description Link
EVfold Evolutionary couplings calculated from correlated mutations in a protein family, used to predict 3D structure from sequences alone and to predict functional residues from coupling strengths. Predicts both globular and transmembrane proteins. Webserver Server
QUARK Monte Carlo fragment assembly On-line server for protein modeling (best for ab initio folding in CASP9) Server
NovaFold Combination of threading and ab initio folding Commercial protein structure prediction application Home page
I-TASSER Threading fragement structure reassembly On-line server for protein modeling Server

download

Selvita Protein Modeling Platform Package of tools for protein modeling Interactive webserver and standalone program including: CABS ab initio modeling Home page
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
CABS-FOLD Server for de novo modeling, can also use alternative templates (consensus modeling). Webserver server
Bhageerath A computational protocol for modeling and predicting protein structures at the atomic level. Webserver Server
Abalone Molecular Dynamics folding Program Example
PEP-FOLD De novo approach, based on a HMM structural alphabet On-line server for peptide structure prediction Server

Secondary structure prediction[edit]

Detailed list of programs can be found at List of protein secondary structure prediction programs

Transmembrane helix prediction[edit]

Name Method Description Link
HMMTOP Hidden Markov Model Webserver/standalone main page
MEMSAT Neural networks and SVMs 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 Hidden Markov Model Webserver/standalone main page
SVMTop2 Support Vector Machines Webserver main page

Signal peptide prediction[edit]

Name Method Description Link
SignalP artificial neural networks and hidden Markov models Webserver/standalone server


See also[edit]