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Protocols

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 citations

 (15)
library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] the use of simulated annealing algorithms, which are based on the general principles that govern protein structure and energetics and therefore does not require a template (e.g. ROSETTA , FRAGFOLD , PROTINFO , FILM ). Each software tool has its specificities and advantages, and use different energy functions and computational methods, but protein 3D structures' building methods generally achieve […]

call_split

Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information

2015
PMCID: 4690985
PMID: 26744735
DOI: 10.1021/acscentsci.5b00251
call_split See protocol

[…] The structural model candidates for the TNH αβγ trimer are generated based on four templates (PDB ID: 3hht, 1ugq, 1ugs, and 1ahj) with dimer models predicted by protinfo ppc server. A 10 ns all-atom molecular dynamics simulation with periodic water box was conducted using NAMD 2.9 with the CHARMM force field., The periodic water box was set up as a layer of 1 […]

library_books

Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding

2014
Retrovirology
PMCID: 4299382
PMID: 25533001
DOI: 10.1186/s12977-014-0115-7

[…] The QUARK, ITASSER, LOMETS, and PROTINFO protein structure prediction servers were used for automated modeling of Rev and are described in [,,,,,]. Default settings were used for the QUARK, ITASSER, and LOMETS servers. The “generate […]

library_books

High intralocus variability and interlocus recombination promote immunological diversity in a minimal major histocompatibility system

2014
BMC Evol Biol
PMCID: 4302578
PMID: 25526691
DOI: 10.1186/s12862-014-0273-1

[…] x 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 confidence: […]

library_books

Structure Prediction of Partial Length Protein Sequences

2013
Int J Mol Sci
PMCID: 3742278
PMID: 23867606
DOI: 10.3390/ijms140714892

[…] e 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 […]

call_split

Homo dimerization and ligand binding by the leucine rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens

2013
BMC Plant Biol
PMCID: 3626623
PMID: 23497186
DOI: 10.1186/1471-2229-13-43
call_split See protocol

[…] 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 by […]


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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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