Protein structure prediction

CDD - Conserved Domain database
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Collection of well-annotated multiple sequence alignments for domains and full-length proteins, available as position-specific score matrices (PSSMs).

Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002 Jan 1;30(1):281-3. PubMed PMID: 11752315. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9. Epub 2010 Nov 24. PubMed PMID: 21109532.

2002

CATH
http://www.cathdb.info/

Structural classification of domains of the proteins from PDB database. Classificatio is done using manual as well as automated procedures.

Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure. 1997 Aug 15;5(8):1093-108. PubMed PMID: 9309224. Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 2007 Jan;35(Database issue):D291-7. Epub 2006 Nov 29. PubMed PMID: 17135200.

1997

3DFold_test
http://phys.protres.ru/resources/predictionA0analogy/3Dfold

Database containing large sets of domains with spatially similar structure and an even larger control sets of spatially dissimilar structure.

Lobanov MIu, Bogatyreva NS, Ivankov DN, Finkel'shtein AV. [Protein structure prediction from analogy. I. New database of spatially similar and dissimilar structures of protein domains for testing and optimization of prediction methods]. Mol Biol (Mosk). 2009 Jul-Aug;43(4):722-32. Russian. PubMed PMID:19807036.

2009

100

3DID - 3D Interacting Domains
http://3did.irbbarcelona.org/index.html

Database of 3D Interaction Domains (3did). This is a collection of domain-domain interactions in proteins with known 3D structure.

Stein A, Russell RB, Aloy P. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D413-7. PubMed PMID: 15608228. Stein A, C\E9ol A, Aloy P. 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2011 Jan;39(Database issue):D718-23. Epub 2010 Oct 21. PubMed PMID: 20965963.

2005

100

DoBo - Domain Boundary Prediction
http://sysbio.rnet.missouri.edu/dobo/

Identifies domain boundries in protein sequences. Uses support vector machine and sequence alignment.

Eickholt J, Deng X, Cheng J. DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. BMC Bioinformatics. 2011 Feb 1;12:43. PubMed PMID: 21284866.

2011

100

Upgraded version of Domac.
Upgraded version of Domac.

Domain Fishing
http://bmm.cancerresearchuk.org/~3djigsaw/dom_fish/

The Server/Suite trues to find out possible domains in the given protein sequence. Uses Pfam, SCOP and swiss prot as reference for domain classification.

Contreras-Moreira B, Bates PA. Domain fishing: a first step in protein comparative modelling. Bioinformatics. 2002 Aug;18(8):1141-2. PubMed PMID: 12176841.

2002

100

Also provides conservation maps of residues in a protein domain family.
Also provides conservation maps of residues in a protein domain family.

DomIns - Domain Insertion database
http://www.domins.org/

Database of domain insertions in known protein structures that are classified in the SCOP database.

Selvam RA, Sasidharan R. DomIns: a web resource for domain insertions in known protein structures. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D193-5. PubMed PMID: 14681392.

2004

100

Gene3D
http://gene3d.biochem.ucl.ac.uk/

Used for CATH domain assignment to an unknown sequence.

Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA. Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res. 2002 Mar;12(3):503-14. PubMed PMID: 11875040. Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C. Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res. 2008 Jan;36(Database issue):D414-8. Epub 2007 Nov 21. PubMed PMID: 18032434.

2002

100

GeneSilico
http://genesilico.pl/meta.

This is a meta Server/Suite used for protein structure prediction. Has multiple tools for primary, secondary and Tertiary Structure Prediction including methods for prediction of transmembrane helix, disordered region and disulfide bonds, etc.

Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-Server/Suite. Nucleic Acids Res. 2003 Jul 1;31(13):3305-7. PubMed PMID: 12824313.

2003

100

Registration and obtaining free license is necessary for every user.
Registration and obtaining free license is necessary for every user.

IntFOLD
http://www.reading.ac.uk/bioinf/IntFOLD/

WebServer/Suite that predicts structure and function of a protein sequence. Includes 5 methods nFOLD4, ModFOLD 3.0, DISOclust 2.0, DomFOLD 2.0 and FunFOLD 1.0 that are used for Tertiary Structure Prediction, model quality assessment, disorder prediction, Domain Predictionand ligand binding site prediction respectively.

Roche DB, Buenavista MT, Tetchner SJ, McGuffin LJ. The IntFOLD Server/Suite: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, Domain Predictionand ligand binding site prediction. Nucleic Acids Res. 2011 Jul;39(Web Server/Suite issue):W171-6. Epub 2011 Mar 31. PubMed PMID: 21459847.

2011

100

For batch jobs, user needs to mail to the university along with a short project description.
For batch jobs, user needs to mail to the university along with a short project description.

JAIL
http://bioinformatics.charite.de/jail/

Classifies the interfaces between domain architectures, protein chains and also between protein and DNA.

GFCnther S, von Eichborn J, May P, Preissner R. JAIL: a structure-based interface library for macromolecules. Nucleic Acids Res. 2009 Jan;37(Database issue):D338-41. Epub 2008 Oct 2. PubMed PMID: 18832369.

2009

100

Meta-DP
http://meta-dp.bioinformatics.buffalo.edu

Domain Predictionmeta Server/Suite. It is coupled to 10 Domain PredictionServer/Suites and can be programmed to include more.

Saini HK, Fischer D. Meta-DP: Domain Predictionmeta-Server/Suite. Bioinformatics. 2005 Jun 15;21(12):2917-20. Epub 2005 Apr 19. PubMed PMID: 15840708.

2005

100

Pfam
http://pfam.sanger.ac.uk/

Database of protein domain families.

Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997 Jul;28(3):405-20. PubMed PMID: 9223186. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. Epub 2009 Nov 17. PubMed PMID: 19920124.

1997

100

PredictProtein
http://www.predictprotein.org

Web based service for sequence analysis which takes squences or alignments and returns various relevent results related to the structure of that sequence as multiple sequence alignments, prosite sequence motifs and predictions of secondary structure, solvent accessibility, transmembrane helics and various other features.

Rost B, Yachdav G, Liu J. The PredictProtein Server/Suite. Nucleic Acids Res. 2004 Jul 1;32(Web Server/Suite issue):W321-6. PubMed PMID: 15215403.

2004

100

PSIPRED Server/Suite
http://bioinf.cs.ucl.ac.uk/psipred/

Structure prediction Server/Suite. Has tools for Secondary Structure Prediction, Transmembrane topology prediction and Fold recognition.

McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction Server/Suite. Bioinformatics. 2000 Apr;16(4):404-5. PubMed PMID: 10869041.

2000

100

For extensive usage, the Server/Suite is available on payment.
For extensive usage, the Server/Suite is available on payment.

PSPP - Protein Structure Prediction Pipeline
http://www.bhsai.org/structure2.html

Protein structure predicion software package, used for comparative modelling, ab initio modelling and fold recognition. Is a collection of more than 20 individual software packages and databases. `

Lee MS, Bondugula R, Desai V, Zavaljevski N, Yeh IC, Wallqvist A, Reifman J. PSPP: a protein structure prediction pipeline for computing clusters. PLoS One. 2009 Jul 16;4(7):e6254. PubMed PMID: 19606223.

2009

100

SAHG - Structural Atlas of Human Genome
http://bird.cbrc.jp/sahg

Structural Atlas of Human Genome is a database of protein structures encoded in human genome. Predicts protein structure through its own structure prediction pipeline, which uses various available tools and algorithms.

Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M. SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res. 2011 Jan;39(Database issue):D487-93. Epub 2010 Nov 3. PubMed PMID: 21051360.

2010

100

Scooby Domain
http://www.ibi.vu.nl/programs/scoobywww/

Used for identification of globular domains in protein sequences based on the length and hydrophobicities of already known domains. Available as a Java applet.

George RA, Lin K, Heringa J. Scooby-domain: prediction of globular domains in protein sequence. Nucleic Acids Res. 2005 Jul 1;33(Web Server/Suite issue):W160-3. PubMed PMID: 15980446.

2005

100

Current version is 2.0, whereas the version of java applet is 1.0
Current version is 2.0, whereas the version of java applet is 1.0

SCRATCH
http://www.ics.uci.edu/~baldig/scratch/index.html

Tertiary Structure Prediction Server/Suite. Includes tools for Secondary Structure Prediction, solvent accessibility of protein, domains and other structural features.

Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction Server/Suite. Nucleic Acids Res. 2005 Jul 1;33(Web Server/Suite issue):W72-6. PubMed PMID: 15980571.

2005

100

The tools in the Server/Suite have individual limitations with respect to sequence length and operating platform.
The tools in the Server/Suite have individual limitations with respect to sequence length and operating platform.