• ProteoWizard

  • Referenced in 2 articles [sw30165]
  • Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several...
  • GeneRAGE

  • Referenced in 5 articles [sw35909]
  • clustering of large protein sequence datasets, such as complete proteomes, into families, according to sequence ... automatic clustering of protein sequence datasets has been developed. This algorithm represents all similarity relationships...
  • iTIS-PseTNC

  • Referenced in 15 articles [sw22449]
  • proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that...
  • integrOmics

  • Referenced in 4 articles [sw28007]
  • transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology...
  • DECOD

  • Referenced in 1 article [sw33137]
  • studies including large-scale sequencing and proteomics. These datasets present new challenges. The first...
  • SpectralNET

  • Referenced in 3 articles [sw26161]
  • modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks ... network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET...
  • pSuc-Lys

  • Referenced in 31 articles [sw16643]
  • acid composition, (2) balancing out skewed training dataset by random sampling, and (3) constructing ... analyze many other problems in computational proteomics...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • computational intensive work for large datasets, e.g., genome-level proteomics and transcriptomics data sets which ... perform cross analysis and integration between several datasets, which might be useful to investigate responses...
  • iLoc-Euk

  • Referenced in 37 articles [sw22434]
  • performed with iLoc-Euk on a benchmark dataset of eukaryotic proteins classified into the following ... useful bioinformatics tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development Also...
  • iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • PTMs in proteins is crucial for dynamic proteome analysis of various human diseases and epigenetic ... rigorous jackknife test and independent dataset test that iMethyl-PseAAC was superior...
  • iCar-PseCp

  • Referenced in 18 articles [sw23951]
  • acid composition, and balancing out skewed training dataset by Monte Carlo sampling to expand positive ... analyze many other problems in computational proteomics...
  • EcmPred

  • Referenced in 1 article [sw22406]
  • training and 77% on the test dataset. EcmPred predicted 15 out of 20 experimentally verified ... proteome, we predicted novel ECM proteins validated with gene ontology and InterPro. The dataset...
  • GlycoMine

  • Referenced in 0 articles [sw25080]
  • linked glycosylation sites in the human proteome. GlycoMine was developed using the random forest algorithm ... well-prepared up-to-date benchmark dataset that encompasses all three types of glycosylation sites ... target proteins by screening the entire human proteome. AVAILABILITY AND IMPLEMENTATION: The webserver, Java ... Applet, user instructions, datasets, and predicted glycosylation sites in the human proteome are freely available...
  • MultiLoc2

  • Referenced in 8 articles [sw22456]
  • subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since ... profiles and Gene Ontology terms. Two different datasets were used for training the system, resulting...
  • RepExplore

  • Referenced in 1 article [sw30166]
  • variance in proteomics and metabolomics data analysis. Summary: High-throughput omics datasets often contain technical...
  • Quokka

  • Referenced in 5 articles [sw27666]
  • family-specific phosphorylation sites in the human proteome. Motivation: Kinase-regulated phosphorylation is a ubiquitous ... date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively...
  • iLoc-Plant

  • Referenced in 18 articles [sw22419]
  • performed with iLoc-Plant on a benchmark dataset of plant proteins classified into the following ... useful bioinformatics tool for Molecular Cell Biology, Proteomics, Systems Biology, and Drug Development...
  • MUSA

  • Referenced in 2 articles [sw35518]
  • σ54-dependent promoter sequences and the second dataset included 54 promoter sequences of up-regulated ... response to phenol, as suggested by quantitative proteomics. The results obtained indicate that this approach...
  • PredGPI

  • Referenced in 3 articles [sw17176]
  • needed for a reliable annotation of whole proteomes. Results: Here we present PredGPI, a prediction ... PredGPI is trained on a non-redundant dataset of experimentally characterized GPI-anchored proteins whose ... rapid and accurate method for screening whole proteomes...
  • canprot

  • Referenced in 0 articles [sw20436]
  • Datasets are collected here for differentially (up- and down-) expressed proteins identified in proteomic studies...