• UniProt

  • Referenced in 136 articles [sw21320]
  • important collection of protein sequences and their annotations, which has doubled in size ... experience design process. We have introduced an annotation score for all entries in UniProt ... relative amount of knowledge known about each protein. These scores will be helpful in identifying...
  • Euk-mPLoc

  • Referenced in 42 articles [sw26860]
  • eukaryotic protein entries that have experimentally observed subcellular location annotations, 2715 have multiple location sites ... number of total eukaryotic protein entries (except those annotated with ”fragment” or those with less ... existing methods for predicting eukaryotic protein subcellular localization are limited in the case of single ... protein entries in the Swiss-Prot database that do not have subcellular location annotations...
  • ESLpred

  • Referenced in 20 articles [sw22403]
  • subcellular localization of proteins is an important step in the functional annotation of genomes ... composition or N-terminal characteristics of the proteins. In this paper, support vector machine ... against the dataset of proteins (experimentally annotated proteins) to predict its subcellular location. In order...
  • Hum-mPLoc

  • Referenced in 26 articles [sw26862]
  • human protein entries that have experimentally observed subcellular location annotations in the Swiss-Prot database ... number of total human protein entries (except those annotated with ”fragment” or those with less ... existing methods for predicting human protein subcellular localization are limited in the case of single ... protein entries in the Swiss-Prot database that do not have subcellular location annotations...
  • IntAct

  • Referenced in 31 articles [sw21665]
  • context of the GO annotations of the interacting proteins. A web service allows direct computational...
  • Hum-PLoc

  • Referenced in 24 articles [sw26863]
  • redundancy and homology bias, none of the proteins investigated here had > or = 25% sequence identity ... trivial utilization of the GO annotations. This ... because, for those proteins with ”subcellular location unknown” annotation in Swiss-Prot database, most (more ... annotated with ”cellular component unknown”. The information and clues for predicting subcellular locations of proteins...
  • STRING

  • Referenced in 34 articles [sw23938]
  • functional systems. Currently, protein interactions and associations are annotated at various levels of detail ... scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe...
  • Virus-ploc

  • Referenced in 14 articles [sw22421]
  • that only 23.5% of viral protein entries are annotated for their subcellular locations in this ... throughput tools for timely annotating the localization of viral proteins within host and virus-infected ... viral protein entries in Swiss-Prot database that do not have subcellular location annotations ... annotated as being uncertain. The results thus obtained have been deposited in a downloadable file...
  • SMART

  • Referenced in 16 articles [sw17187]
  • smart.embl.de/) for the identification and annotation of protein domains, and provides a platform...
  • MultiLoc

  • Referenced in 11 articles [sw35402]
  • MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs ... amino acid composition. Motivation: Functional annotation of unknown proteins is a major goal in proteomics ... annotation is the prediction of a protein’s subcellular localization. Numerous prediction techniques have been...
  • Gpos-PLoc

  • Referenced in 11 articles [sw26870]
  • Gram-positive bacterial proteins from the recent Swiss-Prot database, approximately 57% of these entries ... without subcellular location annotations. In the gene ontology database, the corresponding percentage is approximately ... meaning the percentage of proteins without subcellular component annotations is even higher. With the avalanche ... bacterial protein entries in Swiss-Prot database that either have no subcellular location annotation...
  • PathBLAST

  • Referenced in 9 articles [sw29737]
  • pairs of protein interaction paths, for which proteins of the first path are paired with ... positive interactions and allows for functional annotation of protein interaction pathways based on similarity...
  • pLoc-mAnimal

  • Referenced in 27 articles [sw24438]
  • protein sequences, we are challenged to develop fast and effective method to annotate their subcellular ... easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they...
  • Cytoscape

  • Referenced in 82 articles [sw09080]
  • conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly ... link the network to databases of functional annotations. The Core is extensible through a straightforward ... changes in gene expression, a study of protein complexes involved in cellular recovery...
  • SUPERFAMILY

  • Referenced in 5 articles [sw16889]
  • database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation ... hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily ... evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,478 completely...
  • QPath

  • Referenced in 12 articles [sw35403]
  • interactions. We applied QPath to systematically infer protein pathways in fly using an extensive collection ... derive a first annotated map of conserved protein pathways in fly. Conclusion: Pathway homology searches...
  • pLoc-mVirus

  • Referenced in 23 articles [sw24439]
  • cell. With the explosive growth of protein sequences generated in the postgenomic ... demanded to develop computational tools for timely annotating their subcellular locations based on the sequence ... current study is focused on virus proteins. Although considerable efforts have been made in this...
  • Euk-PLoc

  • Referenced in 24 articles [sw22420]
  • protein entries (excluding fragments) in Swiss-Prot database that do not have subcellular location annotations ... annotated as being uncertain. The large-scale results will be updated twice a year ... include the new entries of eukaryotic proteins and reflect the continuous development of Euk-PLoc...
  • BOMP

  • Referenced in 4 articles [sw11337]
  • when tested on the proteins with SwissProt annotated subcellular localization in Escherichia coli ... sequences to be possible integral β-barrel proteins. Of these, 36 were found by BLAST ... value score < 1e−10) to proteins with annotated subcellular localization in SwissProt. BOMP predicted...
  • EnsemblePail

  • Referenced in 6 articles [sw27725]
  • identification of potential Lysine Acetylation sites from protein sequences. The computational method is based ... Lysine Acetylation sites and more confident annotation of protein Acetylation...