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Structure conservation prediction software tools | Protein structure data analysis

All residues in a protein are not equally important. Some are essential for the proper structure and function of the protein, whereas others can be readily replaced. Conservation analysis is one of the most widely used methods for predicting these…
Blocks Database
Dataset

Blocks Database

Collects ungapped multiple alignments of short regions. Blocks Database was…

Collects ungapped multiple alignments of short regions. Blocks Database was built from sequences of protein families using a fully automated method and allows to detect one or more of blocks…

CDD
Dataset

CDD Conserved Domain Database

Provides a public repository for annotation of proteins. CDD includes more than…

Provides a public repository for annotation of proteins. CDD includes more than 56 000 records from all sources database dispatched into 5 600 multi-model superfamilies. The database incorporates…

Rate4Site
Desktop

Rate4Site

A program for detecting conserved amino-acid sites by computing the relative…

A program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA). The sole obligatory input to Rate4Site is an MSA…

ConPlex
Web

ConPlex

Enables evolutionary conservation analyses of protein interactions within…

Enables evolutionary conservation analyses of protein interactions within protein quaternary structures. ConPlex automatically identifies protein interfaces and carries out evolutionary conservation…

AL2CO
Web

AL2CO

Performs conservation analysis in a comprehensive and systematic way. AL2CO…

Performs conservation analysis in a comprehensive and systematic way. AL2CO calculates a conservation index at each position in a multiple sequence alignment using several methods. The algorithm of…

FuncPatch
Web

FuncPatch

An intuitive web server to perform a fast approximate Bayesian inference of…

An intuitive web server to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures. Both simulations and four case studies based on empirical data…

CDART
Web

CDART Conserved Domain Architecture Retrieval Tool

Uses the domain definitions and annotations from the Conserved Domain Database…

Uses the domain definitions and annotations from the Conserved Domain Database (CDD) (which imports alignments from SMART and Pfam) and RPS-BLAST to allow users to rapidly query the Entrez Protein…

JET
Desktop

JET Joint Evolutionary Trees

Detects very different types of interactions of a protein with another protein,…

Detects very different types of interactions of a protein with another protein, ligands, DNA, and RNA. JET, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary…

CDTree
Desktop

CDTree Conserved Domain Tree

Enables users of the CDD (conserved domain database) resource to examine…

Enables users of the CDD (conserved domain database) resource to examine curated hierarchies. CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users…

Batch cd-search
Web

Batch cd-search Batch conserved domain search

A web-based tool for the detection of structural and functional domains in…

A web-based tool for the detection of structural and functional domains in protein sequences. CD-Search combines the sensitivity of carefully constructed search models based on multiple sequence…

ConSurf
Web

ConSurf

A web-based tool that automatically calculates evolutionary conservation scores…

A web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. ConSurf combines two independent servers (ConSeq and…

ConSurf-DB
Dataset

ConSurf-DB

A repository for evolutionary conservation analysis of the proteins of known…

A repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using…

GP4Rate
Desktop

GP4Rate

A C++ program which combines Gaussian processes and phylogenetics to infer…

A C++ program which combines Gaussian processes and phylogenetics to infer conserved sites in protein tertiary structures. GP4Rate uses the Gaussian process to define a nonparametric prior…

ConSSeq
Web

ConSSeq Consensus Sequence

Represents graphically information about amino acid conservation based on…

Represents graphically information about amino acid conservation based on sequence alignments reported in homology-derived structures of proteins (HSSP). ConSSeq is a web-based application that…

PatchFinder
Web

PatchFinder

A methodology that automatically identifies patches of conserved residues that…

A methodology that automatically identifies patches of conserved residues that are located in close proximity to each other on the protein surface. PatchFinder is based on the following steps: (1)…

Protein…
Desktop
Web

Protein Residue Conservation Prediction

An information-theoretic approach for estimating sequence conservation based on…

An information-theoretic approach for estimating sequence conservation based on Jensen-Shannon divergence. A general heuristic that considers the estimated conservation of sequentially neighboring…

CASP
Dataset

CASP Critical Assessment of Structure Prediction

Gathers information on proteins. CASP is an online resource that assists users…

Gathers information on proteins. CASP is an online resource that assists users in identification of protein structure from sequence. It offers several methods to work on the protein topic and aims to…

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