Tag: Functional Site

Crescendo – Identifying Functional Sites in Proteins

Crescendo

:: DESCRIPTION

Crescendo is a program for identifying functional sites in proteins. It distinguishes structural and functional restraints in evolution in order to identify interaction sites.

::DEVELOPER

LOVELL LAB

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

V. Chelliah, L. Chen, T.L. Blundell and S.C. Lovell
Distinguishing Structural and Functional Restraints in Evolution in Order to Identify Interaction Sites
Journal of Molecular Biology, 342(5):1487-1504, 2004

DNAFSMiner – DNA Functional Site Miner

DNAFSMiner

:: DESCRIPTION

DNAFSMiner is a web-based software toolbox that aims to predict these functional sites in DNA sequences.Currently, there are two software tools. One is called TIS Miner which can be used to predict translation initiation site (TIS) in vertebrate mRNA, cDNA, or DNA sequences. The other is called Poly(A) Signal Miner which can be used to predict polyadenylation (poly(A)) signal in human DNA sequences.

::DEVELOPER

DNAFSMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Mar 1;21(5):671-3. Epub 2004 Jul 29.
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences.
Liu H1, Han H, Li J, Wong L.

SuMo 5.0 – 3D search for Functional Sites

SuMo 5.0

:: DESCRIPTION

SuMo (Surfing the Molecules) is a bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins.

::DEVELOPER

SuMo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Oct 15;21(20):3929-30.
The SuMo server: 3D search for protein functional sites.
Jambon M, Andrieu O, Combet C, Deléage G, Delfaud F, Geourjon C.

FunSiP 0.8.1b – Prediction of Functional Sites in DNA

FunSiP 0.8.1b

:: DESCRIPTION

FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. FunSip is a platform that uses a very general approach towards the classification of functional sites in DNA sequences. The program uses an ab initio approach towards the identification of these sites, and extends SpliceMachine, a previously developed splice site predictor that shows state-of-the-art performance for both donor and acceptor splice site recognition in the human and Arabidopsis thaliana genome.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 FunSiP

:: MORE INFORMATION

Citation:

Van Bel, M., Saeys, Y., Van de Peer, Y. (2008)
FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA.
Bioinformatics 24, 1532-3.

Exit mobile version