• Cytoscape

  • Referenced in 73 articles [sw09080]
  • gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference...
  • MCODE

  • Referenced in 47 articles [sw35748]
  • automated method for finding molecular complexes in large protein interaction networks. Results: This paper describes ... large protein-protein interaction networks that may represent molecular complexes. The method is based ... relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces cerevisiae ... many of which correspond to known protein complexes. The algorithm is not affected...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell...
  • QNet

  • Referenced in 10 articles [sw13845]
  • large scale cross-species comparison of protein complexes, by querying known yeast complexes against...
  • CellProfiler

  • Referenced in 14 articles [sw18751]
  • cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape...
  • SCWRL4

  • Referenced in 7 articles [sw22393]
  • converge on very large proteins or protein complexes or those with very dense interaction graphs...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • yeast proteins. This lead us to the identification of a novel yeast complex that here ... term vid30 complex (vid30c). The observed interaction was confirmed by tandem affinity purification ... ability of PIPE to predict novel protein-protein interactions. We then used PIPE analysis ... study the internal architecture of yeast protein complexes. The data also suggests that a finite...
  • ConsensusPathDB

  • Referenced in 6 articles [sw29342]
  • describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With 155 432 human...
  • SMART

  • Referenced in 16 articles [sw17187]
  • comparative study of complex domain architectures in genes and proteins. The January 2004 release...
  • BindingDB

  • Referenced in 6 articles [sw23141]
  • experimentally determined binding affinities of protein-ligand complexes, for 110 protein targets including isoforms...
  • Graemlin

  • Referenced in 5 articles [sw29736]
  • conserved network topologies other than protein complexes and metabolic pathways. To assess Græmlin’s performance...
  • LIGPLOT

  • Referenced in 5 articles [sw16869]
  • generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file ... show other types of interaction in proteins and nucleic acids. It was designed to facilitate ... rapid inspection of many enzyme complexes, but has found many other applications...
  • SMPDB

  • Referenced in 2 articles [sw29378]
  • relevant organs, subcellular compartments, protein_complex cofactors, protein_complex locations, metabolite locations, chemical structures ... protein_complex quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained ... HMDB or DrugBank and each protein_complex or enzyme complex is hyperlinked to UniProt ... pathway diagrams. Gene, metabolite and protein_complex concentration data can also be visualized through SMPDB...
  • DeepVS

  • Referenced in 4 articles [sw16458]
  • amino acid types obtained from protein-ligand complexes. Our approach introduces the use of atom ... creating distributed vector representations of protein-ligand complexes by modeling the compound...
  • PathBLAST

  • Referenced in 8 articles [sw29737]
  • networks across species to identify protein pathways and complexes that have been conserved by evolution ... high-scoring alignments between pairs of protein interaction paths, for which proteins of the first...
  • KnotProt

  • Referenced in 5 articles [sw21418]
  • with knots or slipknots. The knotting complexity of proteins is presented in the form...
  • NetworkBLAST

  • Referenced in 2 articles [sw34157]
  • protein networks. Summary: The identification of protein complexes is a fundamental challenge in interpreting protein ... server provides a platform for identifying protein complexes in protein-protein interaction networks ... case, NetworkBLAST outputs a set of putative complexes that are evolutionarily conserved across...
  • StSNP

  • Referenced in 3 articles [sw30039]
  • interactions in a multi-protein complex, by increasing/decreasing the activity of the metabolic pathway. Understanding ... sequence, structure data and pathway relations between proteins. The data from NCBI’s SNP database...
  • Negatome

  • Referenced in 3 articles [sw29347]
  • curation of literature and by analysing protein complexes from the PDB. More stringent lists ... much less biased towards functionally dissimilar proteins than the negative data derived by randomly selecting...
  • UniPROBE

  • Referenced in 3 articles [sw18504]
  • Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences ... database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches...