:: DESCRIPTION
dcGOR is an open-source R package for analysing domain-centric ontologies and annotations (dcGO and others)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS Comput Biol. 2014 Oct 30;10(10):e1003929. doi: 10.1371/journal.pcbi.1003929. eCollection 2014.
dcGOR: an R package for analysing ontologies and protein domain annotations.
Fang H
:: DESCRIPTION
T-RMSD web server (tree-based on root-mean-square deviation) is a service allowing the online computation of structure-based protein classification.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
T-RMSD: a web server for automated fine-grained protein structural classification.
Magis C, Di Tommaso P, Notredame C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W358-62. doi: 10.1093/nar/gkt383.
:: DESCRIPTION
PhenoFam performs gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. The tool is designed to analyse complete sets of results from quantitative high-throughput studies (gene expression microarrays, functional RNAi screens, etc.) without prior pre-filtering or hits-selection steps.
::DEVELOPER
Frank Buchholz , Max Planck Institute of Molecular Cell Biology and Genetics.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 May 17;11:254. doi: 10.1186/1471-2105-11-254.
PhenoFam – gene set enrichment analysis through protein structural information.
Paszkowski-Rogacz M, Slabicki M, Pisabarro MT, Buchholz F.
:: DESCRIPTION
Domain Fishing looks for recognizable protein domains in your amino acid sequence. It tries to find good sequence matches from your sequence to every protein domain defined in PFAM , a very comprehensive database that increasingly covers the protein sequence landscape.
::DEVELOPER
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Contreras-Moreira,B. and Bates,P.A. (2002).
Domain Fishing: a first step in protein comparative modelling.
Bioinformatics 18: 1141-1142.
:: DESCRIPTION
DOMpro predicts domain locations using a 1D-RNN. DOMpro takes an input the sequence profile, predicted secondary structure, and predicted relative solvent accessiblity. The output of the 1D-RNN is a classification for each residue as being in a domain boundary region or not. The domains are then infered from this output.
::DEVELOPER
Institute for Genomics and Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J. Cheng, M. Sweredoski, & P. Baldi.
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.
Knowledge Discovery and Data Mining, vol. 13, no. 1, pp. 1-20, (2006)