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TPDB specifications

Information


Unique identifier OMICS_24687
Name TPDB
Alternative name Target Protein DataBase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Robert Hanzlik

Publications for Target Protein DataBase

TPDB citations

 (7)
library_books

LRRK2 promotes the activation of NLRC4 inflammasome during Salmonella Typhimurium infection

2017
PMCID: 5626397
PMID: 28821568
DOI: 10.1084/jem.20170014

[…] and digested with in situ trypsin. Tryptic peptides were analyzed with a QExactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific). Tandem mass spectra were searched against a target protein database using the MASCOT search engine (Matrix Science Ltd). […]

library_books

A Graph Centric Approach for Metagenome Guided Peptide and Protein Identification in Metaproteomics

2016
PLoS Comput Biol
PMCID: 5137872
PMID: 27918579
DOI: 10.1371/journal.pcbi.1005224

[…] solely on contigs []. Here, we attempt to predict protein coding genes directly from the sequences in the de Bruijn graph, including the proteins that span multiple edges in the graph, to expand the target protein database for metaproteomic data analysis. We implemented an algorithm that takes as input the de Bruijn graph of a metagenome assembly, traverses the graph in a depth-first search (DFS) […]

library_books

Using reverse docking to identify potential targets for ginsenosides

2016
PMCID: 5628352
PMID: 29021701
DOI: 10.1016/j.jgr.2016.10.005

[…] ion, angiogenesis modulation, and cytotoxicity . In this work, we utilized the reverse docking technique to elucidate and/or confirm therapeutic values and side effects of ginsenosides by screening a target protein database against them. Chen et al have used a reverse docking method, called INVDOCK, to extract possible drug targets by predicting interactions between compounds including ginsenosid […]

library_books

Comparative Analysis of Lacinutrix Genomes and Their Association with Bacterial Habitat

2016
PLoS One
PMCID: 4755562
PMID: 26882010
DOI: 10.1371/journal.pone.0148889

[…] Blast2GO []. For the analysis of gene presence/absence, sequencing reads were re-mapped onto the assemblies using Bowtie 2 (Ver. 2.2.6) [], and unmapped read were identified using BLASTx against the target protein database. The amino acid sequences of the presence gene were also identified using tBLASTx against the target draft genome sequence. […]

library_books

A new scoring function for top down spectral deconvolution

2014
BMC Genomics
PMCID: 4378558
PMID: 25523396
DOI: 10.1186/1471-2164-15-1140

[…] e for the parameter settings of MS-Align+ and the three tools.) The EC proteome database was downloaded from the Swiss-Prot database, and a shuffled database of the same size was concatenated to the target protein database for estimation of FDRs. With 1% protein level FDR, MS-Deconv+ coupled with MS-Align+ identified more spectra (1,585 in HCD and 1,223 in ETD) than MS-Deconv (1,543 in HCD and 1, […]

library_books

Molecular modeling, dynamics studies and virtual screening of Fructose 1, 6 biphosphate aldolase II in community acquired methicillin resistant Staphylococcus aureus (CA MRSA)

2013
Bioinformation
PMCID: 3569604
PMID: 23423142
DOI: 10.6026/97320630009158

[…] retrieved from the UniProtKB database (Uniprot accession no: P67478) (www.uniprot.org). The length of target protein was 286 amino acid residues. In order to find the most similar template(s) for the target protein, database searching was performed against the PDB database using the BLASTp program []. Based on high sequence identity (76%) a template (pdb id: 3Q94) was selected, subsequently multip […]

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TPDB institution(s)
Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA; Applied Bioinformatics Lab, University of Kansas, Lawrence, KS, USA
TPDB funding source(s)
Supported by the U.S. National Institutes of Health (GM-21784).

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