• PROSITE

  • Referenced in 36 articles [sw17326]
  • dedicated to the identification of protein families and domains, PROSITE is the first one created ... documentation briefly describing the protein family or domain they are designed to detect. The close ... relationship of PROSITE with the SWISS-PROT protein database allows the evaluation of the sensitivity ... characteristics and the techniques of family and domain identification used by PROSITE are reviewed...
  • SMART

  • Referenced in 16 articles [sw17187]
  • identification and annotation of protein domains, and provides a platform for the comparative study ... complex domain architectures in genes and proteins. The January ... release of SMART contains 685 protein domains. New developments in SMART are centred ... exon structure within the context of protein domain structure, and to align these displays...
  • InterProScan

  • Referenced in 17 articles [sw17336]
  • InterProScan: protein domains identifier. InterProScan [E. M. Zdobnov and R. Apweiler (2001) Bioinformatics ... tool that combines different protein signature recognition methods from the InterPro [N. J. Mulder...
  • MEME

  • Referenced in 14 articles [sw15711]
  • transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence ... patterns that occur in the DNA or protein sequences provided by the user. Users...
  • iTOL

  • Referenced in 9 articles [sw33187]
  • data such as genome sizes or protein domain repertoires can be mapped onto the tree...
  • GeneRAGE

  • Referenced in 5 articles [sw35909]
  • subsequent detection and resolution of multi-domain proteins. Results: A new algorithm for the automatic ... programming alignment algorithm. Detection of multi-domain protein families and further false positive relationships within ... representation for each protein in the dataset. Initial clusters containing multi-domain families, are split ... presence of multi-domain proteins are minimized, allowing more precise clustering information to be obtained...
  • iPfam

  • Referenced in 8 articles [sw29349]
  • iPfam: a database of protein family and domain interactions found in the Protein Data Bank ... Pfam domain interactions based on known 3D structures that are found in the Protein Data ... molecular level. Previously, the iPfam domaindomain interaction data was integrated within the Pfam database ... separation between the protein family and interactions datasets. In addition to domaindomain interactions, iPfam...
  • WebGestalt

  • Referenced in 7 articles [sw17514]
  • chromosome distribution, metabolic and signaling pathways, protein domain information and publications. The statistics module recommends...
  • ProClust

  • Referenced in 6 articles [sw35761]
  • values based on the length of the protein sequences compared. Additionally, the significance of alignment ... joint data set includes all multi-domain proteins, which contain the SCOP domains that...
  • DOMpro

  • Referenced in 3 articles [sw17202]
  • DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks ... Protein domains are the structural and functional units of proteins. The ability to parse protein ... recursive neural networks, to develop a protein domain predictor called DOMpro. DOMpro predicts protein domains ... with respect to the single-domain proteins and sensitivity of 59% and specificity...
  • EVEREST

  • Referenced in 3 articles [sw22975]
  • EVEREST: a collection of evolutionary conserved protein domains. Protein domains are subunits of proteins that ... capture the essence of a protein domain, and several systems that identify protein domains ... system that performs the task automatically, using protein sequence alone. Herein we describe EVEREST release ... those sources, graphically visualizing the domain organization of the proteins in the family. The website...
  • REACH

  • Referenced in 6 articles [sw00788]
  • scale elastic network model in single-domain proteins using the variance–covariance matrix obtained from...
  • SUPERFAMILY

  • Referenced in 5 articles [sw16889]
  • hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily ... together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences...
  • IUPred

  • Referenced in 8 articles [sw16915]
  • estimated energy content. Summary: Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three...
  • DIMA

  • Referenced in 4 articles [sw26868]
  • DIMA web resource--exploring the protein domain network. Conserved domains represent essential building blocks ... most known proteins. Owing to their role as modular components carrying out specific functions they ... physical interactions. We have previously shown that domain interaction networks provide substantially novel information with ... protein chains. In this work we present a comprehensive web resource for exploring the Domain...
  • ProTDB

  • Referenced in 20 articles [sw13843]
  • from two application areas: protein chemistry data from the bioinformatics domain, and information extraction data...
  • KineticDB

  • Referenced in 3 articles [sw16246]
  • folding process. Comparison with experimental protein folding rates has been the main tool for validation ... folding kinetics measurements of single-domain proteins and separate protein domains as well as short ... includes data on about 90 unique proteins and many mutants that have been systematically accumulated...
  • MotifMiner

  • Referenced in 7 articles [sw35523]
  • system by analyzing several disparate domains, including protein, drug, and MD simulation datasets...
  • MUMMALS

  • Referenced in 4 articles [sw13110]
  • computed pairwise structure alignments of divergent protein domains is superior to smaller but carefully curated...
  • OrthoDB

  • Referenced in 4 articles [sw22979]
  • logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene...