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PP specifications

Information


Unique identifier OMICS_07135
Name PP
Alternative name PredictProtein
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
High performance computing Yes
Maintained Yes

Publications for PredictProtein

library_books

The PredictProtein server

2004 Nucleic Acids Res
PMCID: 441515
PMID: 15215403
DOI: 10.1093/nar/gkh377

PP citations

 (265)
library_books

Identification and characterization of smallest pore forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

2018
BMC Biochem
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9

[…] hypothetical protein CUR_1714 and hypothetical protein CUR_1715) sequences were submitted to different servers such as PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred), MINNOU (http://minnou.cchmc.org/), PredictProtein (http://www.predictprotein.org/), TMRPres2D (http://bioinformatics.biol.uoa.gr/TMRPres2D/) and PORTER (http://distill.ucd.ie/porter/) for predictions of its secondary structure. All sec […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] e development and AON process were obtained by comparison with orthologous genes in other legumes using multiple protein sequence alignment in COBALT (https://www.ncbi.nlm.nih.gov/tools/cobalt/). The PredictProtein was used to perform GO terms, protein-protein and protein-DNA binding sites and sub-cellular localization (Yachdav et al., ). The SWISS-MODEL was used to predict protein tertiary struct […]

library_books

Detection of functional protein domains by unbiased genome wide forward genetic screening

2018
Sci Rep
PMCID: 5906580
PMID: 29670134
DOI: 10.1038/s41598-018-24400-4

[…] n analyzed. Both these methods suggested that the vast majority of the TOP1 mutations we identified in camptothecin resistant strains were likely to produce deleterious effects (PROVEAN score < −2.5; PredictProtein score >50) (Fig. ). Notably, missense mutations located in the C-terminal domain of Top1 affected both conserved and non-conserved residues and were primarily positioned in the vicinity […]

call_split

Ehrlichia chaffeensis TRP120 nucleomodulin binds DNA with disordered tandem repeat domain

2018
PLoS One
PMCID: 5895000
PMID: 29641592
DOI: 10.1371/journal.pone.0194891
call_split See protocol

[…] red [], SsPro [], Porter [], and Gor4 [] were used to predict the secondary structure content of a single 80 amino acid TR unit. Disordered region prediction programs PrDOS [], IUPred [], DisEMBL [], PredictProtein [] were used to predict the disordered regions in TRP120. […]

call_split

Natural Resistance Associated Macrophage Protein Is Involved in Immune Response of Blunt Snout Bream, Megalobrama amblycephala

2018
PMCID: 5946104
PMID: 29596379
DOI: 10.3390/cells7040027
call_split See protocol

[…] of the positive clones was performed at Sangon Biotech Co., Ltd. (Shanghai, China). All sequences were assembled to obtain the full-length cDNA sequence of maNramp. Protein structure was predicted by PredictProtein (PP) software and Expert Protein Analysis System (ExPASy). Multiple alignment of amino acids sequences of Nramp protein from M. amblycephala and other species was carried out using the […]

library_books

Transmembrane E3 ligase RNF183 mediates ER stress induced apoptosis by degrading Bcl xL

2018
Proc Natl Acad Sci U S A
PMCID: 5866564
PMID: 29507230
DOI: 10.1073/pnas.1716439115

[…] entify apoptosis-promoting RING finger proteins (RNFs), we found that overexpression of RNF183 increases apoptosis () and reduces cell survival (SI Appendix, Fig. S1). Primary sequence analysis using PredictProtein () revealed that human RNF183 contains an N-terminal RING-type zinc finger (residues 13–60) and a C-terminal transmembrane domain (). RNF183 transcripts were ubiquitous (SI Appendix, Fi […]

Citations

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PP institution(s)
Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universitat Munchen), Garching/Munich, Germany; Biosof LLC, New York, NY, USA; TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universitat Munchen), Garching/Munich, Germany; New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY, USA; Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Freising, Germany; The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Luxembourg University & Luxembourg Centre for Systems Biomedicine, Luxembourg; CMBI, NCMLS, Radboudumc Nijmegen Medical Centre, Nijmegen, Netherlands; Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Biochemistry and Molecular Biophysics & New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY, USA; Institute for Advanced Study (TUM-IAS), Garching/Munich, Germany; Institute for Food and Plant Sciences WZW-Weihenstephan, Freising, Germany
PP funding source(s)
Supported by Alexander von Humboldt foundation through the German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung).

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