funClust – Identification of Local Functional Motifs in non-homologous Protein Structures

funClust

:: DESCRIPTION

funClust is a web server for the identification of local functional motifs in a set of non homologous protein structures.You can submit a set of protein structures deemed to share a common function (e. g. they bind similar ligands, interact with similar protein interfaces or share an enzymatic activity).

::DEVELOPER

Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S2. doi: 10.1186/1471-2105-9-S2-S2.
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.
Ausiello G1, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M.

OMiMa – Identify Functional Motifs in DNA or Protein Sequences

OMiMa

:: DESCRIPTION

The OMiMa (the Optimized Mixture Markov model) System is a computational tool for identifying functional motifs in DNA or protein sequences. OMiMa System is based on the Optimized Mixture of Markov models that are able to incorporate most dependencies within a motif. Most important, OMiMa is capable to adjust model complexity according to motif dependency structures, so it can minimize model complexity without compromising prediction accuracy. OMiMa uses our fast Markov chain optimization method, the Directed Neighbor-Joining (DNJ), which makes OMiMa more computationally efficent.

::DEVELOPER

Weichun Huang at Biostatistics Branch, the National Institute of Environmental Health Sciences (NIEHS), NIH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OMiMa

:: MORE INFORMATION

Citation

Weichun Huang, David M Umbach, Uwe Ohler, Leping Li.
Optimized mixed Markov models for motif identification.
BMC Bioinformatics 2006, 7:279