neXtProt: organizing protein knowledge in the context of human proteome projects.

PubWeight™: 1.80‹?› | Rank: Top 3%

🔗 View Article (PMID 23205526)

Published in J Proteome Res on December 03, 2012

Authors

Pascale Gaudet1, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek, Olivier Evalet, Alain Gateau, Anne Gleizes, Mario Pereira, Monique Zahn-Zabal, Catherine Zwahlen, Amos Bairoch, Lydie Lane

Author Affiliations

1: CALIPHO Group, SIB-Swiss Institute of Bioinformatics, Faculty of Medicine, University of Geneva, CMU-1, rue Michel Servet 1211 Geneva 4, Switzerland.

Articles citing this

STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res (2014) 10.79

A draft map of the human proteome. Nature (2014) 6.58

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res (2014) 2.66

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res (2013) 1.76

State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52

Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics (2015) 1.44

The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res (2015) 1.42

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J Proteome Res (2015) 1.26

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics (2014) 0.98

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. J Proteome Res (2015) 0.98

MOPED enables discoveries through consistently processed proteomics data. J Proteome Res (2013) 0.89

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database (Oxford) (2015) 0.88

Transcriptome analysis of the dihydrotestosterone-exposed fetal rat gubernaculum identifies common androgen and insulin-like 3 targets. Biol Reprod (2013) 0.87

What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. Mol Biol Cell (2014) 0.84

Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Res (2014) 0.84

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res (2014) 0.83

The strategy, organization, and progress of the HUPO Human Proteome Project. J Proteomics (2013) 0.82

The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res (2016) 0.81

Shared resources, shared costs--leveraging biocuration resources. Database (Oxford) (2015) 0.80

The impact of structural genomics: the first quindecennial. J Struct Funct Genomics (2016) 0.79

Changes in mitochondrial carriers exhibit stress-specific signatures in INS-1Eβ-cells exposed to glucose versus fatty acids. PLoS One (2013) 0.79

TAILS N-terminomic and proteomic datasets of healthy human dental pulp. Data Brief (2015) 0.77

Urine Proteome Biomarkers in Kidney Diseases. I. Limits, Perspectives, and First Focus on Normal Urine. Biomark Insights (2016) 0.76

Integrating omics technologies to study pulmonary physiology and pathology at the systems level. Cell Physiol Biochem (2014) 0.76

Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells. Data Brief (2015) 0.75

Accelerating the search for the missing proteins in the human proteome. Nat Commun (2017) 0.75

Articles by these authors

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80

UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05

InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07

The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72

The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70

InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53

ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39

IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02

The PROSITE database, its status in 2002. Nucleic Acids Res (2002) 14.71

Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem (2003) 13.44

New developments in the InterPro database. Nucleic Acids Res (2007) 12.49

Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89

Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics (2009) 8.87

PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform (2002) 8.77

The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiol Biochem (2004) 8.59

The PROSITE database. Nucleic Acids Res (2006) 8.11

PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res (2009) 7.47

Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11

UniProtKB/Swiss-Prot. Methods Mol Biol (2007) 7.05

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res (2006) 6.13

The 20 years of PROSITE. Nucleic Acids Res (2007) 6.06

ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics (2002) 5.81

The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19

High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform (2002) 4.95

IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65

A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61

ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics (2005) 3.41

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res (2008) 3.29

Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91

MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Res (2007) 2.77

InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66

The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics (2002) 2.51

UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45

Protein sequence databases. Curr Opin Chem Biol (2004) 2.43

A positive feedback loop stabilizes the guanine-nucleotide exchange factor Cdc24 at sites of polarization. EMBO J (2002) 2.39

The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res (2008) 2.14

The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat (2004) 1.97

Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97

FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification. Proteomics (2002) 1.83

Efficient lentiviral vector-mediated control of HIV-1 replication in CD4 lymphocytes from diverse HIV+ infected patients grouped according to CD4 count and viral load. Mol Ther (2004) 1.80

neXtProt: a knowledge platform for human proteins. Nucleic Acids Res (2011) 1.77

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res (2013) 1.76

Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics (2004) 1.76

ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res (2010) 1.66

MyHits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Res (2004) 1.64

Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C R Biol (2005) 1.54

Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat (2008) 1.50

Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase. Toxicon (2004) 1.47

The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors. Structure (2004) 1.42

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. J Proteomics (2008) 1.38

Down-regulation of ECRG4, a candidate tumor suppressor gene, in human breast cancer. PLoS One (2011) 1.27

Rapid evolution of cancer/testis genes on the X chromosome. BMC Genomics (2007) 1.26

Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24

OpenFluDB, a database for human and animal influenza virus. Database (Oxford) (2010) 1.20

Standard guidelines for the chromosome-centric human proteome project. J Proteome Res (2012) 1.20

Plant protein annotation in the UniProt Knowledgebase. Plant Physiol (2005) 1.15

Phytochrome-mediated light signalling in Arabidopsis. Curr Opin Plant Biol (2004) 1.09

Use of the chicken lysozyme 5' matrix attachment region to generate high producer CHO cell lines. Biotechnol Bioeng (2005) 1.08

Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. J Proteomics (2013) 1.07

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics (2009) 1.04

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res (2012) 1.03

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics (2004) 0.98

Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins. Proteomics (2004) 0.96

The human proteome project: Current state and future direction. Mol Cell Proteomics (2011) 0.96

Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature. Pharmacogenet Genomics (2009) 0.95

In vitro and in silico processes to identify differentially expressed proteins. Proteomics (2004) 0.93

Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway. PLoS One (2012) 0.91

Insight into molecular interactions between two PB1 domains. J Mol Biol (2004) 0.89

The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. Database (Oxford) (2014) 0.88

A large-scale protein-function database. Nat Chem Biol (2010) 0.86

Experiments in searching small proteins in unannotated large eukaryotic genomes. J Proteome Res (2005) 0.81

Animal Toxins: How is Complexity Represented in Databases? Toxins (Basel) (2010) 0.79

Combining bioinformatics and MS-based proteomics: clinical implications. Expert Rev Proteomics (2014) 0.79

Cosine modulated HSQC: a rapid determination of (3)J(HNHalpha) scalar couplings in (15)N-labeled proteins. J Magn Reson (2002) 0.79

[From genome to proteome--aim of human proteomics]. Seikagaku (2004) 0.77

Post-translational modifications: a challenge for proteomics and bioinformatics. Proteomics (2004) 0.76

In vitro antimicrobial effects of 3 root canal sealers on Actinomyces radicidentis. P R Health Sci J (2014) 0.75

The ingestion of a Nectandra membranacea extract changes the bioavailability of technetium-99m radiobiocomplex in rat organs. Biol Res (2007) 0.75