11/24/2020 List of protein structure prediction software - Wikipedia

List of protein structure prediction

software
This list of protein structure prediction software summarizes
notable 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
Software list
Homology modeling
Threading/fold recognition
Ab initio structure prediction
Secondary structure prediction
See also
References Constituent amino-acids can be
analyzed to predict secondary,
tertiary and quaternary protein
structure.
Software list
Below is a list which separates programs according to the method used for structure prediction.

Homology modeling

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Name Method Description Link

Automated
remote homology detection, protein webserver and server and download (http://raptorx.uchicag
RaptorX
3D modeling, binding site prediction Downloadable o.edu/)
program
BLAST search,
T-Coffee
wraps external programs into
Biskit alignment, and project site (http://biskit.sf.net/)
automated workflow
MODELLER
construction
Template detection, alignment, 3D Automated server (http://www.fundp.ac.be/urbm/bioinfo/
ESyPred3D
modeling webserver esypred/)
Energy calculations and protein Downloadable
FoldX download (http://foldx.crg.es/)
design program
Webserver with
job manager,
Remote template detection, automatically
Phyre and
alignment, 3D modeling, multi- updated fold server (http://www.sbg.bio.ic.ac.uk/~phyre/)
Phyre2
templates, ab initio library, genome
searching and
other facilities
server (http://arquivo.pt/wayback/201605140
83149/http%3A//toolkit.tuebingen.mpg.de/hh
Interactive
Template detection, alignment, 3D pred) download (ftp://ftp.tuebingen.mpg.de/p
HHpred webserver with
modeling ub/protevo/HHsearch) article (http://nar.oxfor
help facility
djournals.org/cgi/reprint/33/suppl_2/W244?ijk
ey=FuurmQ3jgumZ6AU&keytype=ref)
Standalone
program mainly download (https://salilab.org/modeller/)
MODELLER Satisfaction of spatial restraints
in Fortran and Server (https://salilab.org/modweb/)
Python
Standalone
Satisfaction of contact and distance program mainly download (https://github.com/multicom-toolb
CONFOLD
restraints in Fortran and ox/CONFOLD)
Perl
Template identification, use of
multiple templates and accounting Proprietary
MOE
for other environments (e.g. platform,
(Molecular
excluded ligand volumes), loop supported on site (http://www.chemcomp.com)
Operating
modelling, rotamer libraries for Windows, Linux
Environment)
sidechain conformations, relaxation and Mac
using MM forcefields.
Rosetta homology modeling and ab
ROBETTA initio fragment assembly with Ginzu Webserver server (http://robetta.bakerlab.org/)
domain prediction
Protein tertiary
BHAGEERATH- Combination of ab initio folding and server (http://www.scfbio-iitd.res.in/bhageerat
structure
H homology methods h/bhageerath_h.jsp)
predictions
Automated
webserver
SWISS-MODEL Local similarity/fragment assembly server (http://swissmodel.expasy.org/)
(based on
ProModII)

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Name Method Description Link

Detection of templates, alignment,
Graphical
modeling incl. ligands and Home page (http://www.yasara.org/) CASP8
Yasara interface or text
oligomers, hybridization of model results (http://www.yasara.org/casp8.htm)
mode (clusters)
fragments
Molecular dynamics simulation
based on template-guided, Automated
AWSEM-Suite server (http://awsem.rice.edu)
coevolutionary-enhanced optimized webserver
folding landscapes[1]

Threading/fold recognition

Name Method Description Link

Remote template detection, single-
template and multi-template Webserver with job
threading, totally different from and manager, download (http://raptorx.uchicago.edu/)
RaptorX
much better than the old program automatically server (http://raptorx.uchicago.edu/)
RAPTOR designed by the same updated fold library
group
server (https://toolkit.tuebingen.mpg.de/#/tools/h
Interactive hpred) download (ftp://ftp.tuebingen.mpg.de/pu
Template detection, alignment, 3D
HHpred webserver with help b/protevo/HHsearch) article (http://bioinformatic
modeling
facility s.oxfordjournals.org/cgi/content/abstract/bti125?i
jkey=38Cp1qeK4zozg&keytype=ref)
Webserver with job
manager,
Phyre Remote template detection,
automatically
and alignment, 3D modeling, multi- server (http://www.sbg.bio.ic.ac.uk/~phyre2/)
updated fold library,
Phyre2 templates, ab initio
genome searching
and other facilities

Ab initio structure prediction

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Name Method Description Link

Server (https://yanglab.na
trRosetta is an algorithm for fast and accurate de novo Webserver and nkai.edu.cn/trRosetta/)
protein structure prediction. It builds the protein source codes. It
structure based on direct energy minimizations with a takes about one download (https://yan
trRosetta
restrained Rosetta. The restraints include inter- hour to fold
residue distance and orientation distributions, proteins with glab.nankai.edu.cn/tr
predicted by a deep residual neural network. ~300 AAs Rosetta/download/)

Server (http://zhanglab.cc
mb.med.umich.edu/I-TASS
ER/)
On-line server
I-TASSER Threading fragment structure reassembly for protein download (http://zhan
modeling glab.ccmb.med.umic
h.edu/I-TASSER/down
load)

Rosetta homology modeling and ab initio fragment server (http://new.robetta.o

ROBETTA Webserver
assembly with Ginzu domain prediction rg/)
Distributed-computing implementation of Rosetta Downloadable main page (http://boinc.ba
Rosetta@home
algorithm program kerlab.org/rosetta/)
Example (http://www.biom
Abalone Molecular Dynamics folding Program olecular-modeling.com/Ab
alone/Protein-folding.html)

Secondary structure prediction

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

See also
List of protein secondary structure prediction programs
Comparison of nucleic acid simulation software
List of software for molecular mechanics modeling
Molecular design software
Protein design

References
1. Jin, Shikai; Contessoto, Vinicius G; Chen, Mingchen; Schafer, Nicholas P; Lu, Wei; Chen, Xun;
Bueno, Carlos; Hajitaheri, Arya; Sirovetz, Brian J; Davtyan, Aram; Papoian, Garegin A; Tsai, Min-
Yeh; Wolynes, Peter G (2 July 2020). "AWSEM-Suite: a protein structure prediction server based on
template-guided, coevolutionary-enhanced optimized folding landscapes" (https://www.ncbi.nlm.nih.g
ov/pmc/articles/PMC7319565). Nucleic Acids Research. 48 (W1): W25–W30.
doi:10.1093/nar/gkaa356 (https://doi.org/10.1093%2Fnar%2Fgkaa356). PMC 7319565 (https://www.
ncbi.nlm.nih.gov/pmc/articles/PMC7319565). PMID 32383764 (https://pubmed.ncbi.nlm.nih.gov/3238
3764).

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