List of protein structure prediction software

This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction

Protein structure prediction

Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...

, including homology modeling

Homology modeling

Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...

, protein threading, ab initio methods, secondary structure prediction

Secondary structure prediction

Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure...

, and transmembrane helix and signal peptide prediction.

Homology modeling

Name	Method	Description	Link
RaptorX	remote homology detection, accurate alignment, 3D modeling	Automated webserver	server
3D-JIGSAW	Fragment assembly	Automated webserver	server
Biskit Biskit Biskit is an open source software package written in Python.The package facilitates research in Structural bioinformatics and molecular modelling...	wraps external programs into automated workflow	BLAST BLAST In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences... search, T-Coffee T-Coffee T-Coffee is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment... alignment, and MODELLER MODELLER MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures . It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create... 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 ESyPred3D ESyPred3D is an automated Homology modeling program. The method gets benefit of the increased alignment performances of an alignment strategy that uses neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs...	Template detection, alignment, 3D modeling	Automated webserver	server
FoldX FoldX FoldX is a protein design algorithm that uses an empirical force field. It can determine the energetic effect of point mutations as well as the interaction energy of protein complexes...	Energy calculations and protein design	Downloadable program	download
GeneSilico GeneSilico Laboratory of Bioinformatics and Protein Engineering in International Institute of Molecular and Cell Biology in Warsaw, Poland.-Fields of research:* Protein and nucleic acid structure modeling* Discovery and analysis of enzymes that act on DNA or RNA...	Consensus template search/fragment assembly	Webserver	server
Geno3D	Satisfaction of spatial restraints	Automated webserver	server
HHpred HHpred / HHsearch HHsearch is a program for protein sequence searching that is free for non-commercial use. HHpred is a free protein function and protein structure prediction server based on the HHsearch method...	Template detection, alignment, 3D modeling	Interactive webserver with help facility	server [ftp://ftp.tuebingen.mpg.de/pub/protevo/HHsearch 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 MODELLER MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures . It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create...	Satisfaction of spatial restraints	Standalone program in Python Python (programming language) Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...	download
Phyre and Phyre2 Phyre / Phyre2 Phyre and Phyre2 are web-based services for protein structure prediction that are free for non-commercial use. Phyre is among the most popular methods for protein structure prediction having been cited over 1000 times...	Remote template detection, alignment, 3D modeling, multi-templates, ab initio	Webserver with job manager, automatically updated fold library, genome searching and other facilities	server
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 BLAST In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences... 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 What If What if? is a question that often is used in the context of:* Counterfactual history* Alternate history* UchroniaWhat If may refer to:- Literature :* "What If—", a fantasy short story by Isaac Asimov...	Position specific rotamers	Standalone program and webinterface	Home page Webinterface

Threading/fold recognition

Name	Method	Description	Link
RaptorX RaptorX / software for protein modeling and analysis RaptorX for protein modeling and analysisRaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. Other popular methods include HHpredHHpred / HHsearch and...	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 HHpred / HHsearch HHsearch is a program for protein sequence searching that is free for non-commercial use. HHpred is a free protein function and protein structure prediction server based on the HHsearch method...	Template detection, alignment, 3D modeling	Interactive webserver with help facility	server [ftp://ftp.tuebingen.mpg.de/pub/protevo/HHsearch download] article
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 Phyre / Phyre2 Phyre and Phyre2 are web-based services for protein structure prediction that are free for non-commercial use. Phyre is among the most popular methods for protein structure prediction having been cited over 1000 times...	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 RAPTOR (software) RAPTOR is protein threading software used for protein structure prediction, given a primary sequence.-Protein threading vs. homology modeling:Researchers attempting to solve a protein's structure start their a study with little more than a protein sequence...	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
SPARKSx/SP series	3D structure modeling by Fold recognition according to Sequence profiles and structural profiles	Webserver	Server

Ab initio structure prediction

Name	Method	Description	Link
QUARK Quark A quark is an elementary particle and a fundamental constituent of matter. Quarks combine to form composite particles called hadrons, the most stable of which are protons and neutrons, the components of atomic nuclei. Due to a phenomenon known as color confinement, quarks are never directly...	Monte Carlo fragment assembly	On-line server for protein modeling (best for ab initio folding in CASP9)	Server
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@home Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing platform, run by the Baker laboratory at the University of Washington...	Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction	Webserver	server
Rosetta@home Rosetta@home Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing platform, run by the Baker laboratory at the University of Washington...	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
Abalone Abalone (molecular mechanics) Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit water or in implicit water models...	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

Name	Method	Description	Link
NetSurfP	Profile-based neural network	Webserver	server
GOR Gor Gor , the Counter-Earth, is the alternate-world setting for a series of 30 novels by John Norman that combine philosophy, erotica and science fiction...	Information theory/Bayesian inference Bayesian inference In statistics, Bayesian inference is a method of statistical inference. It is often used in science and engineering to determine model parameters, make predictions about unknown variables, and to perform model selection...	Many implementations	Basic GOR GOR V
Jpred	Neural network Neural network The term neural network was traditionally used to refer to a network or circuit of biological neurons. The modern usage of the term often refers to artificial neural networks, which are composed of artificial neurons or nodes... 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 Neural Networks Neural Networks is the official journal of the three oldest societies dedicated to research in neural networks: International Neural Network Society, European Neural Network Society and Japanese Neural Network Society, published by Elsevier... which perform an analysis on output obtained from PSI-BLAST	Webserver	server
YASSPP	Cascaded SVM Support vector machine A support vector machine is a concept in statistics and computer science for a set of related supervised learning methods that analyze data and recognize patterns, used for classification and regression analysis... -based predictor using PSI-BLAST profiles	Webserver	server
RaptorX-SS8 RaptorX / software for protein modeling and analysis RaptorX for protein modeling and analysisRaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. Other popular methods include HHpredHHpred / HHsearch and...	predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles	Webserver/downloadable program	server download
PSSpred	Multiple backpropagation Backpropagation Backpropagation is a common method of teaching artificial neural networks how to perform a given task. Arthur E. Bryson and Yu-Chi Ho described it as a multi-stage dynamic system optimization method in 1969 . It wasn't until 1974 and later, when applied in the context of neural networks and... neural network Neural network The term neural network was traditionally used to refer to a network or circuit of biological neurons. The modern usage of the term often refers to artificial neural networks, which are composed of artificial neurons or nodes... predictors from PSI-BLAST profiles	Webserver/downloadable program	server and downloadable program

Transmembrane helix prediction

Name	Method	Description	Link
HMMTOP	Hidden Markov Model Hidden Markov model A hidden Markov model is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved states. An HMM can be considered as the simplest dynamic Bayesian network. The mathematics behind the HMM was developed by L. E...	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 Hidden Markov model A hidden Markov model is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved states. An HMM can be considered as the simplest dynamic Bayesian network. The mathematics behind the HMM was developed by L. E...	Webserver/standalone	main page

Signal peptide prediction

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

Homology modeling

Threading/fold recognition

Ab initio structure prediction

Secondary structure prediction

Transmembrane helix prediction

Signal peptide prediction

See also