PP pipeline

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 IN pipelines

 (3)
2013
PMCID: 3705618
PMID: 23847402
DOI: 10.6026/97320630009471

[…] and evaluation tools (data not shown) were used, but the following tools were relied upon more for greater accuracy. the secondary structure elements were determined using the dobo [11] and predictprotein (results not shown) [12] severs. for protein homology modeling, we used online available tool called itasser [13]. this server uses the threading technique to predict the 3d models. […]

2012
PMCID: 3466273
PMID: 23056574
DOI: 10.1371/journal.pone.0047047

[…] 1j5b) was used as template for molecular modeling [38]. the pa-map model shows α-helical conformation (figure 3b); this has also been observed in data obtained through prediction servers, such as predictprotein and sopma, which presented 92 and 88% of the amino acid residues favoring this conformation [39], [40]. the procheck summary of pa-map showed that 95.8% of amino acid residues […]

2007
PMCID: 2241624
PMID: 17996046
DOI: 10.1186/1471-2091-8-23

[…] matches were evaluated in terms of an e-value, which is an estimation of the probability of finding a better match by chance. secondary structure predictions were performed using the predictprotein server [25,26]. alkb active center illustrations (figure 1. bottom) were generated with pymol [27]., 2og (2-oxoglutarate), alkb (alkylated dna repair protein), ests (expressed sequence […]

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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