COPRED – Prediction of Fold, GO Molecular Function and Functional Residues at the Domain Level

COPRED

:: DESCRIPTION

COPRED is a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked.

::DEVELOPER

Computational Systems Biology Group (CNB-CSIC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 15;29(14):1811-2. doi: 10.1093/bioinformatics/btt283. Epub 2013 May 29.
COPRED: prediction of fold, GO molecular function and functional residues at the domain level.
López D1, Pazos F.

MCdet – Detection of Functional Residues

MCdet

:: DESCRIPTION

MCdet implements a method for detecting positions in multiple sequence alignments with a “function-dependent” conservation pattern. These positions have been shown to be related to functionality, and they complement the fully conserved positions as predictors of functionality from sequence information

::DEVELOPER

Antonio Rausell (arausell@cnio.es)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MCdet

:: MORE INFORMATION

Citation

Florencio Pazos, Antonio Rausell & Alfonso Valencia. (2006).
Phylogeny-independent detection of functional residues.
Bioinformatics. 22(12):1440-1448.

TreeDet v2 – Predicting Functional Residues in Protein Sequence Alignments

TreeDet v2

:: DESCRIPTION

The TreeDet (Tree Determinant) Server is the first release of a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in either user-uploaded or automatically generated multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm.

::DEVELOPER

the Bioinformatics Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser (do not support IE)

:: DOWNLOAD

:: MORE INFORMATION

Citation

TreeDet: a web server to explore sequence space.
Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W110-5.

Graphlet kernel 1.01 – Annotate Functional Residues in Protein Structures

Graphlet kernel 1.01

:: DESCRIPTION

Graphlet kernelis a supervised learning framework for annotating functional residues in protein structures. Each residue is represented as a vector of counts of labeled non‐isomorphic subgraphs (called graphlets) in the protein contact graph, and a similarity measure between two vertices is expressed as the inner product of their respective count vectors

::DEVELOPER

the Algorithms and Computational Biology Lab

:: REQUIREMENTS

Linux

:: DOWNLOAD

Graphlet kernel

:: MORE INFORMATION

Citation:

Vladimir Vacic, Lilia Iakoucheva, Stefano Lonardi, and Predrag Radivojac
“Graphlet kernels for prediction of functional residues in protein structures”
Journal of Computational Biology. 17(1):55-72. (2010)