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3D structure similarity searching software tools | Protein data analysis

3D protein structure similarity searching is one of the important processes performed in structural bioinformatics, since it allows for protein function identification and reconstruction of phylogeny for weakly related organisms. Due to the…
Dali server
Web

Dali server

A network service for comparing protein structures in 3D. Dali server provides…

A network service for comparing protein structures in 3D. Dali server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure…

iSARST
Web

iSARST

A web service for efficient protein structural similarity searches. iSARST…

A web service for efficient protein structural similarity searches. iSARST gives tables listing co-linear or circularly permuted homologs of the query proteins and a functional summary of the best…

MATRAS
Web

MATRAS MArkovian TRAnsition of Structure evolution

A web server for comparing protein 3D structures using the program Matras. An…

A web server for comparing protein 3D structures using the program Matras. An advantage of Matras is its structure similarity score, which is defined as the log-odds of the probabilities, similar to…

RAPIDO
Web
ProteinDBS
Web

ProteinDBS Protein DataBase Search engine

Applies computer visualization techniques to extract the predominant visual…

Applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains.…

deconSTRUCT
Web

deconSTRUCT

Offers an interface to a protein database search engine, usable for a general…

Offers an interface to a protein database search engine, usable for a general purpose detection of similar protein (sub)structures. Initially, it deconstructs the query structure into its secondary…

YAKUSA
Web

YAKUSA

A program designed for rapid scanning of a structural database with a query…

A program designed for rapid scanning of a structural database with a query protein structure.

HDInsight4Psi
Desktop

HDInsight4Psi

Possesses several unique features that positively affect computational…

Possesses several unique features that positively affect computational efficiency of the system. The most important characteristics of HDInsight4Psi are: the use of sequence files, possible…

SALAMI
Web

SALAMI

Searches the protein data bank, for similar chains, calculates structural…

Searches the protein data bank, for similar chains, calculates structural alignments and generates a list of structurally related proteins. SALAMI has the advantage that it relies on chain…

fastSCOP
Web

fastSCOP

Identifies the structural domains and determines the evolutionary superfamilies…

Identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. fastSCOP uses 3D-BLAST to scan quickly a large structural classification database and the…

BCscore
Desktop

BCscore

Allows the search of both similar and mirror conformations. BC score has…

Allows the search of both similar and mirror conformations. BC score has several interesting properties. In particular, it is independent to any rotation of the structures and consequently its…

Cloud4Psi
Desktop

Cloud4Psi Cloud for Protein Similarity

Enables researchers to search for protein structure similarities by using a…

Enables researchers to search for protein structure similarities by using a combination of three algorithms: jCE, jFATCAT-rigid and jFATCAT-flexible. Cloud4Psi allows for the completion of the task…

3D-Blast
Web

3D-Blast

A shape-density based protein structure search and alignment tool which uses…

A shape-density based protein structure search and alignment tool which uses the Hex docking spherical polar Fourier (SPF) correlation technique.

GOSSIP
Web

GOSSIP GlObal Structural SuperposItion of Proteins

Detects similarities between structures down to a certain cutoff (a parameter…

Detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment…

DaliLite
Desktop
Web

DaliLite

A program for pairwise structure comparison and for structure database…

A program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server. A web interface is provided to view the…

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…

TOPSCAN
Web

TOPSCAN

Reduces a protein to a series of secondary structure elements (SSEs) and adds…

Reduces a protein to a series of secondary structure elements (SSEs) and adds information to the SSE descriptors such as relative direction, accessibility, adjacency to the previous SSE, length and…

pvSOAR
Web

pvSOAR pocket and void Surfaces Of Amino acid Residues

Recognizes similar surface regions in three-dimensional protein structures.…

Recognizes similar surface regions in three-dimensional protein structures. pvSOAR compares local sequences, local shapes and local orientations between residues located on a geometrically defined…

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