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GeneSilico Metaserver

This is a gateway to various methods for protein structure prediction. If you submit a single protein sequence or a multiple sequence alignment (hereafter called a "target"), you should obtain the following predictions:

Primary structure: domains identified by HmmPfam and HHSearchCDD

Secondary structure: helical/extended/other conformation (H/E/-) sspro4, cdm, psipred, fdm, jnet, prof, gor, spine, sable, pssfinder, sspred, sspal, nnssp, ssp, NetSurfP, SOPRANO

Transmembrane helices: Phobius, MEMSAT3, TMpred, HMMTOP, DAS, MINNOU, OCTOPUS, TMHMM2.0

Disordered regions: DisEMBL,RONN, IUPRED, POODLE-L, GLOBPLOT, DISPROT(VSL2), PrDOS, DISOPRED2, Spritz, disPRO, Pdisorder, Spritz, iPDA, POODLE-S (calculated consensus is CASP8 winning method in the category).

Disulfide bonds: DiANNA, DISULFIND, DBCP and DIpro2.0

Nucleic acid binding residues in proteins: BindN, BindN+, DISIS, DP-Bind, PPRInt, and our meta-predictor for RNA-binding residues (cons3best) - for details see here

Tertiary structure: alignments of the target sequence to sequences of proteins with known structures, identified by protein fold-recognition (FR) methods. The Pcons consensus server will evaluate to which extent the FR alignments agree with each other and if a particular fold can be singled out.

From FR alignments you can automatically generate crude three-dimensional models (without variable loops). You can also select a subset of alignments that belong to a particular fold and submit them to our FRankenstein server, which will splice and recombine the crude models to produce a cute little monster protein model that hopefully resembles the true structure.

Models produced by our server are scored by COLORADO3D. Use "color by temperature factor" option in RASMOL to visualize regions likely to be correct (blue) and those that may be wrong (red). Please remember that all theoretical models must be taken with a grain of salt - and even the most confident ones should be carefully verified.

Please cite:

Whenever disorder prediction used: Kozlowski LP, Bujnicki JM. MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics. 2012 May 24;13(1):111.

For meta-predictor of RNA-binding residues (cons3best): Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM. Computational methods for prediction of protein-RNA interactions. J Struct Biol. 2012; 179(3):261-8

Main citation: Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003; 31: 3305-3307

Important technical note:

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Presently we provide access to following FR servers:

 
 
 

Happy predicting !

 
      Fri, 06 May 2016 05:31:18 +0200  / Copyright© 2002-2012 genesilico.pl