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Structural motif search software tools | Protein data analysis

Detection of structural motif of residues in protein structures allows identification of structural or functional similarity between proteins. In the field of protein engineering, structural motif identification is essential to select protein…
PBE
Web

PBE Protein Block Expert

Allows users to perform comparison and analysis for protein structure. PBE…

Allows users to perform comparison and analysis for protein structure. PBE offers a platform composed of 10 tools which can accomplish various tasks such as (i) Encode protein structure into PBs…

ProSMoS
Web

ProSMoS Protein Structure Motif Search

Finds exact structure patterns in proteins while not being very sensitive to…

Finds exact structure patterns in proteins while not being very sensitive to the details of packing and orientation of secondary structural elements (SSEs), thus detecting very distant possible…

GPS-ARM
Desktop
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…

ReMUS
Web
Desktop

ReMUS Reinforced Merging for Unique Segments

Allows users to identify sequential unique peptide segments in related protein…

Allows users to identify sequential unique peptide segments in related protein sequences. ReMUS exists in both web application and standalone software. Studied peptide segments can be visualized in…

PatternQuery
Web

PatternQuery

Well defined biomacromolecular patterns such as binding sites, catalytic sites,…

Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. PatternQuery…

BCSearch
Web

BCSearch

Facilitates large-scale mining of protein structures. BCSearch undergoes…

Facilitates large-scale mining of protein structures. BCSearch undergoes several tens of thousands of comparisons per second. It performs a search for similar fragment search within large collections…

Fragment Finder
Web

Fragment Finder

A web-based interactive computing server which can be used to retrieve…

A web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally…

GYM
Web

GYM

Predicts helix-turn-helix motifs. GYM is also able to detect Homeodomain…

Predicts helix-turn-helix motifs. GYM is also able to detect Homeodomain motifs. It uses an efficient screening process that permits to avoid the generation of most infrequent patterns. The tool…

MALISAM
Dataset

MALISAM Manual ALIgnments for Structurally Analogous Motifs

A database of pairwise, structure-based alignments for structurally analogous…

A database of pairwise, structure-based alignments for structurally analogous motifs in proteins. Applications of this database may range from protein evolution studies, e.g. development of remote…

SPRITE
Web

SPRITE 3D Search for PRotein sITEs

A protein structural motif database searching program. Users can upload a PDB…

A protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements…

ASSAM
Web

ASSAM Amino acid pattern Search for Substructures And Motifs

Searches for patterns of amino acid side chains in 3D space within PDB…

Searches for patterns of amino acid side chains in 3D space within PDB structures. The searches are based on distances between the amino side chains which are represented as pseudoatom vectors. This…

IMAAAGINE
Web

IMAAAGINE

Allows the interrogation of the Protein Data Bank for hypothetical 3D side…

Allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a…

RASMOT-3D PRO
Web

RASMOT-3D PRO Recursive Automatic Search of MOTif in 3D structures of PROteins

Performs a systematic search in 3D structures of protein for a set of residues…

Performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology. Comparison is based on Calpha and Cbeta atoms in two steps: inter-atomic distances and…

TopSearch
Web

TopSearch

A powerful gateway to protein structures and their structural relationships.…

A powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural…

Erebus
Web

Erebus

Searches the entire Protein Data Bank (PDB) for a given substructure defined by…

Searches the entire Protein Data Bank (PDB) for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. Erebus produces the list of proteins…

ProFit
Web
Desktop

ProFit

Allows users to fit protein least squares of two or more protein structures.…

Allows users to fit protein least squares of two or more protein structures. ProFit offers features for flexible specification of fitting zones and atoms, calculation of Residue Monitoring System…

FoldMiner
Web

FoldMiner

Detects global and local motifs in a database of proteins without the need for…

Detects global and local motifs in a database of proteins without the need for multiple structure or sequence alignments and without relying on prior classification of proteins into families.…

Sumo
Web

Sumo SUgar Motif search

Permits the identification of carbohydrate structures motifs classified in the…

Permits the identification of carbohydrate structures motifs classified in the literature. Sumo concerns carbohydrate structure given in LINUCS or in IUPAC nomenclature.

iMotifs
Web

iMotifs in silico Structural Analysis of Sequence Motifs in Proteins

Analyses sequence motif among multiple protein data banks (PDBs). iMotifs is a…

Analyses sequence motif among multiple protein data banks (PDBs). iMotifs is a module of the iRDP Web Server that implements a sequence motif based structural analysis approach to generate a detailed…

Wrappy
Desktop

Wrappy

Reports such indicators as z-score, i.e. the number of standard deviations an…

Reports such indicators as z-score, i.e. the number of standard deviations an observation is above or below the expected mean value. Wrappy is a dehydron calculator plugin for PyMOL. Dehydrons are…

LFMPro
Desktop

LFMPro Local Feature Mining in Proteins

Identifies family-specific local sites and their associated features. LFMPro…

Identifies family-specific local sites and their associated features. LFMPro uses feature vectors associated with local neighborhoods to provide a comprehensive sampling of the protein space. The…

Protein…
Web

Protein segment finder

A search engine that uses a compact database to quickly identify protein…

A search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints. The database contains information such as…

SA-Mot
Web

SA-Mot Structural Alphabet Motif

A web server for the extraction and location of structural motifs of interest…

A web server for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent…

Superimpose
Web

Superimpose

Performs structural similarity searches with a preference towards 3D…

Performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g.…

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