Protinfo protocols

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Protinfo specifications

Information


Unique identifier OMICS_14396
Name Protinfo
Interface Web user interface
Restrictions to use None
Input data Protein sequences
Input format PDB
Output data Tertiary prediction module
Output format CASP
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ram Samudrala <>

Publications for Protinfo

Protinfo in pipeline

2005
PMCID: 1074308
PMID: 15805122
DOI: 10.1093/nar/gki327

[…] of the model., only publicly available servers that provide a description of the underlying algorithm are listed. results obtained in livebench-7 are also displayed if available. results for the protinfo-cm server are not presented because of late predictions. servers are colored blue (sequence only methods), red (hybrid methods) and black (structure meta predictors). the ‘code’ column shows […]


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Protinfo in publications

 (9)
PMCID: 4299382
PMID: 25533001
DOI: 10.1186/s12977-014-0115-7

[…] different algorithms (table ). these include the quark server, which implements an ab initio algorithm [,]; the itasser and lomets servers, which implement threading-based algorithms [,]; and the protinfo server, which implements an homology modeling algorithm []. examination of the predicted models revealed significant variation in their overall shapes (table ): 52% of the rev165 models […]

PMCID: 4302578
PMID: 25526691
DOI: 10.1186/s12862-014-0273-1

[…] of the seahorse was reconstructed via homology modeling of the full-length mh class iiα and iiβ loci to the previously determined crystallographic structure of the mouse mh class ii molecule, using protinfo ppc []. inferred protein surface models of target and database sequences were annotated and visualized in chimera v1.6.2 []., protinfo ppc returned five significant hits (structure […]

PMCID: 3742278
PMID: 23867606
DOI: 10.3390/ijms140714892

[…] i-tasser standalone package was downloaded from the zhang lab website and used without modification on the benchmarking setting to generate models for each input sequence. a modified version of the protinfo comparative modeling application [] that omitted the loop building step and selected templates using hhsearch [] (protinfocm/hh) were also applied to the benchmarking dataset. templates used […]

PMCID: 3626623
PMID: 23497186
DOI: 10.1186/1471-2229-13-43

[…] snap (http://www.hiv.lanl.gov/content/sequence/snap/snap.html)., the first model of gmrlk18-1 structure was generated using the ramp software suite of programs (http://compbio.washington.edu; http://protinfo.compbio.washington.edu). the initial template and the corresponding sequence alignments of gmrlk18-1 were chosen from the 3d-jury server (http://bioinfo.pl). the best template was decided […]

PMCID: 3670735
PMID: 23360665
DOI: 10.1093/molbev/mst017

[…] salmon igfbps were inferred using prosite (). for all 19 proteins, nbp and cbp were submitted along with mature salmon igf1 and igf2 (respective accession numbers aaa18211 and ef432854) to the protinfo ppc webserver () and a pdb file of the template (rcsb accession: 2dsr). pdb files for all models are available on request to d.j.m. model quality was assessed using tools available […]


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Protinfo institution(s)
Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
Protinfo funding source(s)
This work was supported in part by a Searle Scholar Award, NSF Grant DBI-0217241, NIH Grant GM068152 and the University of Washington’s Advanced Technology Initiative in Infectious Diseases.

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