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CharProtDB: a database of experimentally characterized protein annotations

R. Madupu, A. Richter, R. J. Dodson, L. Brinkac, D. Harkins, S. Durkin, S. Shrivastava, G. Sutton, D. Haft
2011 Nucleic Acids Research  
CharProtDB (http://www.jcvi.org/charprotdb/) is a curated database of biochemically characterized proteins.  ...  Each annotation is referenced with the source; ideally a journal reference, or, if imported and lacking one, the original database source.  ...  a 'source' database marked as curated but without fully traceable experimental validation with added Gene Ontology annotation data. 8396 experimentally characterized proteins curated from scientific literature  ... 
doi:10.1093/nar/gkr1133 pmid:22140108 pmcid:PMC3245046 fatcat:bt5qedijejatvoffq7dq7q4f5y

Curated BLAST for Genomes [article]

Morgan Price, Adam Arkin
2019 bioRxiv   pre-print
In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant  ...  Given a query such as an enzyme's name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the  ...  Only the experimentally characterized proteins are included. • CharProtDB, a database of characterized proteins (Madupu et al. 2012) .  ... 
doi:10.1101/533430 fatcat:xamaixdlbjbavpoupzfwdtp3aa

Curated BLAST for Genomes

Morgan N. Price, Adam P. Arkin, Casey S. Greene
2019 mSystems  
In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant  ...  Given a query such as an enzyme's name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the  ...  Only the experimentally characterized proteins are included. • CharProtDB, a database of characterized proteins (17) . • EcoCyc, a database of genes in Escherichia coli K-12 (18) . • MetaCyc, a database  ... 
doi:10.1128/msystems.00072-19 pmid:30944879 pmcid:PMC6435814 fatcat:ruuie43itrdnnjkfjkowt2yd3u

PaperBLAST: Text-mining papers for information about homologs [article]

Morgan N Price, Adam P. Arkin
2017 bioRxiv   pre-print
Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature.  ...  Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators.  ...  To check the completeness of PaperBLAST, we examined experimentally-characterized proteins from two other resources: MetaCyc version 19.5 (Caspi et al. 2010) and the characterized proteins database CharProtDB  ... 
doi:10.1101/133041 fatcat:rti5csbjjbhtpmzxf37fgdrqsu

PaperBLAST: Text Mining Papers for Information about Homologs

Morgan N. Price, Adam P. Arkin, Morgan G. I. Langille
2017 mSystems  
Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature.  ...  Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers.  ...  We also examined experimentally characterized proteins from two other resources: MetaCyc version 19.5 (27) and the characterized-protein database CharProtDB (28) .  ... 
doi:10.1128/msystems.00039-17 pmid:28845458 pmcid:PMC5557654 fatcat:xpcwjz2qsnfarg5emlgnnwoyte

The COMBREX Project: Design, Methodology, and Initial Results

Brian P. Anton, Yi-Chien Chang, Peter Brown, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Zhenjun Hu, Niels Klitgord, Ami Levy-Moonshine, Almaz Maksad, Varun Mazumdar, Mark McGettrick (+62 others)
2013 PLoS Biology  
We have assembled preliminary data through collaboration with UniProt and with CharProtDB, a partially curated set of proteins with experimental evidence assembled by JCVI to serve as a source of evidence  ...  REBASE 1,058 COMBREX 16 CharProtDB 8,574 a Table S1 S1 Summary of proteins examined by COMBREX-funded projects.  ...  This group is by far the largest contributor, and COMBREX views any annotation or assignment of protein function that is not explicitly based on the experimental testing of that protein as a prediction  ... 
doi:10.1371/journal.pbio.1001638 pmid:24013487 pmcid:PMC3754883 fatcat:khsfkpyngjgc3mz6gr3fo7owhq

GapMind: Automated annotation of amino acid biosynthesis [article]

Morgan N Price, Adam M Deutschbauer, Adam P. Arkin
2019 biorxiv/medrxiv   pre-print
To avoid error-prone "transitive" annotations, GapMind relies primarily on a database of experimentally-characterized proteins.  ...  If a potential gap in the genome of interest is also a gap in a related microbe that can grow in minimal media, GapMind marks the gap as "known."  ...  This work was performed by ENIGMA, a Scientific Focus Area Program supported by the U.S.  ... 
doi:10.1101/741918 fatcat:sbfi7immz5arpiq7urnoplbtlq

GapMind: Automated Annotation of Amino Acid Biosynthesis

Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin, Steven J. Hallam
2020 mSystems  
To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins.  ...  GapMind should aid the identification of microbial growth requirements. IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins).  ...  This work was performed by ENIGMA, a Scientific Focus Area Program supported by the U.S.  ... 
doi:10.1128/msystems.00291-20 pmid:32576650 fatcat:2kpvdyqcjnehlmz6nmyol33bim

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

M. Y. Galperin, X. M. Fernandez-Suarez
2011 Nucleic Acids Research  
The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI  ...  papers on the recently launched BioSample databases that store sample information for a variety of database resources  ...  Other highlights include CharProtDB, a database of experimentally characterized proteins that is used for genome annotation at the J.  ... 
doi:10.1093/nar/gkr1196 pmid:22144685 pmcid:PMC3245068 fatcat:ez36c3s6nbdsbdtrp4lucw2rwq

Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity

Jessica N. Ricaldi, Derrick E. Fouts, Jeremy D. Selengut, Derek M. Harkins, Kailash P. Patra, Angelo Moreno, Jason S. Lehmann, Janaki Purushe, Ravi Sanka, Michael Torres, Nicholas J. Webster, Joseph M. Vinetz (+2 others)
2012 PLoS Neglected Tropical Diseases  
Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these  ...  We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include .90 such genes.  ...  Each protein was assigned a descriptive common name coming from an HMM name, a JCVI database of experimentally characterized proteins (CharProtDB) [32] , or from a best BER match protein.  ... 
doi:10.1371/journal.pntd.0001853 pmid:23145189 pmcid:PMC3493377 fatcat:g5chvehuvzdkno3sejshsbq55u

Structured RNAs and synteny regions in the pig genome

Christian Anthon, Hakim Tafer, Jakob H Havgaard, Bo Thomsen, Jakob Hedegaard, Stefan E Seemann, Sachin Pundhir, Stephanie Kehr, Sebastian Bartschat, Mathilde Nielsen, Rasmus O Nielsen, Merete Fredholm (+2 others)
2014 BMC Genomics  
Results: We present a comprehensive annotation of structured RNAs in the pig genome.  ...  Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups.  ...  A recent conservative effort to characterize proteins, CharProtDB, contains only 213 human entries [47] , approximately one percent of the total number of protein coding genes.  ... 
doi:10.1186/1471-2164-15-459 pmid:24917120 pmcid:PMC4124155 fatcat:e7lm3yec2ndjnbtsc35hclnqca

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

Morgan N Price, Adam M Deutschbauer, Adam P Arkin
2022
We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources.  ...  GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes.  ...  GapMind relies on known pathways (mostly from MetaCyc [7] ) and a database of experimentally-characterized proteins.  ... 
doi:10.1371/journal.pgen.1010156 pmid:35417463 pmcid:PMC9007349 fatcat:bthr46iejnfplpam32ksa23hhu

Probabilistic Reconstruction and Comparative Systems Biology of Microbial Metabolism

German Plata Caviedes
2017
In this context, I next describe GLOBUS, a probabilistic method for genome-wide biochemical annotations.  ...  With the number of sequenced microbial species soon to be in the tens of thousands, we are in a unique position to investigate microbial function, ecology, and evolution on a large scale.  ...  CharProtDB [16] , a database of experimentally determined protein functions, contained a little over sixteen thousand proteins from 1588 organisms when it was published in 2012.  ... 
doi:10.7916/d80c534r fatcat:i6wxprdfsfh5zmn5duj33kv72i