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Specificity-determining site software tools | Protein sequence analysis

Specificity-determining sites (SDS) are the key positions of a protein family that show a specific conservation of amino acids, related to the subfamily members of that family. SDS play crucial role in developing functional variation within the…
SubSite
Web

SubSite

Allows the user to identify subfamily determining sites (SDS) within a protein…

Allows the user to identify subfamily determining sites (SDS) within a protein family. SubSite takes two different approaches to identify a SDS site. At first SubSite estimates the average relative…

DIVERGE
Desktop

DIVERGE

A software system for phylogeny-based analyses of protein family evolution and…

A software system for phylogeny-based analyses of protein family evolution and functional divergence. It provides a suite of statistical tools for selection and prioritization of the amino acid sites…

Sequence…
Web

Sequence Harmony

An entropy-based method, which accurately detects subfamily specific functional…

An entropy-based method, which accurately detects subfamily specific functional sites from a multiple sequence alignment. The algorithm implements a new formula, able to score compositional…

proteinkeys
Web

proteinkeys

Predicts functional residues in a protein. The statistical entropy for…

Predicts functional residues in a protein. The statistical entropy for individual subfamilies are calculated and optimized to find the subfamily-specific site distributions in an alignment.

SPrOS
Web

SPrOS Specificity Projection On Sequence

Estimates the specificity of residues to user-defined groups. SPrOS is based on…

Estimates the specificity of residues to user-defined groups. SPrOS is based on a local sequence comparison method. It can recognize the amino acid residues associated with the functional groups of…

INTREPID
Desktop
Web

INTREPID

An information-theoretic approach for functional site identification that…

An information-theoretic approach for functional site identification that exploits the information in large diverse multiple sequence alignments (MSAs). INTREPID uses a traversal of the phylogeny in…

SPEER-SERVER
Desktop
Web

SPEER-SERVER

A web server that encodes the specific conservation pattern of amino acid types…

A web server that encodes the specific conservation pattern of amino acid types in a protein family to identify the specificity determining sites (SDS). The specific conservation pattern is predicted…

Multi-Harmony
Web

Multi-Harmony

Provides simplified and powerful interactive access to improved Sequence…

Provides simplified and powerful interactive access to improved Sequence Harmony (SH) and multi-Relief (mR) methods for detection of sub-family specific residues in alignments. You can input your…

TreeDet
Web

TreeDet Tree Determinant

A system designed to integrate results from methods that predict functional…

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…

SDPpred
Web

SDPpred Specificity Determining Position prediction

A tool for prediction of residues in protein sequences that determine the…

A tool for prediction of residues in protein sequences that determine the proteins' functional specificity. SDPpred is designed for analysis of protein families whose members have biochemically…

FunShift
Dataset

FunShift

Provides functional shift (divergence) analysis between the subfamilies of a…

Provides functional shift (divergence) analysis between the subfamilies of a protein domain family. The present release uses protein domain families in Pfam (Version 12.0). Each family was divided…

ET
Web

ET Evolutionary Trace

Ranks amino acid residues in a protein sequence by their relative evolutionary…

Ranks amino acid residues in a protein sequence by their relative evolutionary importance, and when a structure is available for that protein, it also can display a structural map of where top-ranked…

Xdet/MTreedet
Desktop

Xdet/MTreedet

A flexible method that uses Spearman rank-order correlation to find functional…

A flexible method that uses Spearman rank-order correlation to find functional similarity between residue columns among protein families. Different types of biological matrices can be used to…

SPEL
Desktop

SPEL Specificity Positions by Evolutionary Likelihood

An approach to detect positions that are likely to be functional specificity…

An approach to detect positions that are likely to be functional specificity determinants. SPEL, which does not require subgroup definition, takes a multiple sequence alignment of a protein family as…

ASMC
Desktop

ASMC Active Sites Modeling and Clustering

An unsupervised method to classify sequences using structural information of…

An unsupervised method to classify sequences using structural information of protein pockets. The method predicts functional amino-acids by proposing active site SDP residues (Specificity Determining…

multi-RELIEF
Web

multi-RELIEF

An approach for identifying specificity residues that is based on RELIEF, a…

An approach for identifying specificity residues that is based on RELIEF, a state-of-the-art Machine-Learning technique for feature weighting. It estimates the expected 'local' functional…

GroupSim
Desktop

GroupSim

Protein specificity determining position (SDP) predictions and data. The…

Protein specificity determining position (SDP) predictions and data. The average similarity between each pair of amino acids within a subgroup is calculated using a similarity matrix to obtain a…

Spial
Web

Spial Specificity in alignments

Takes a pair of multiple sequence alignments as input and produces an output…

Takes a pair of multiple sequence alignments as input and produces an output that highlights positions which are conserved in both alignments (the consensus), and positions which are specific to…

AMAS
Web

AMAS

Flexible set of amino acid physico-chemical descriptors are used to get SDS.…

Flexible set of amino acid physico-chemical descriptors are used to get SDS. This server allows you to run AMAS on your own multiple sequence alignment.

SDPsite
Web

SDPsite

A tool for identification of protein active and other functional sites, based…

A tool for identification of protein active and other functional sites, based on spatial clustering of SDPs (specificity-determining positions) with CPs (conserved positions). The analysis begins…

SDPfox
Desktop
Web

SDPfox

Provides a phylogeny-independent method for prediction of…

Provides a phylogeny-independent method for prediction of specificity-determining positions (SDPs) and grouping sequences into functional sub-groups. You may use the form below to conduct a training…

BADASP
Desktop

BADASP Burst After Duplication with Ancestral Sequence Predictions

A software package for identifying sites that may confer subfamily-specific…

A software package for identifying sites that may confer subfamily-specific biological functions in protein families following functional divergence of duplicated proteins. A given protein phylogeny…

SDR server
Web

SDR server

Automatically predicts specificity determining residues (SDRs) in the proteins…

Automatically predicts specificity determining residues (SDRs) in the proteins using mutual information and Monte Carlo simulations. SDR web server will automatically map results of predictions on…

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