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.
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
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.
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