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Structure comparison software tools | Protein structures

Quantitative comparison of two structures of the same biological macromolecule or complex is a very common but by no means trivial task. One such example is the comparison of a model with the experimentally determined (reference) structure.Source…
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…

EFICAz
Web
Desktop

EFICAz Enzyme Function Inference by a Combined Approach

Allows users to study the proteomic scale inference of enzyme function. EFICAz…

Allows users to study the proteomic scale inference of enzyme function. EFICAz can identify functionally discriminating residue (FDR) as residues that discriminate the members of a homo-functional…

GPCRHMM
Web
Desktop

GPCRHMM G Protein-Coupled Receptors by Hidden Markov Model

Allows user to visualize protein sequence features. GPCRHMM offers several…

Allows user to visualize protein sequence features. GPCRHMM offers several advantages: users can zoom in on a region and zoom-dependent sequence rendering displays residues automatically at a…

ProteMiner-SSM
Web

ProteMiner-SSM

Provides efficient analysis of similar protein tertiary substructures.…

Provides efficient analysis of similar protein tertiary substructures. ProteMiner-SSM is a web server that carries out analysis in two steps. In the first step, a filtering process based on an…

CAD-score
Web

CAD-score

Contact area-based comparison of structures and interfaces of proteins, nucleic…

Contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

SphereGrinder
Desktop

SphereGrinder

Permits to obtain accurate model quality information for either individual or…

Permits to obtain accurate model quality information for either individual or multiple uploaded models at the different levels of accuracy. SphereGrinder allows to evaluate structures from different…

The LabelHash…
Web
Desktop

The LabelHash Server

A server and tools designed for largescale substructure comparison. The…

A server and tools designed for largescale substructure comparison. The LabelHash Server predicts the function of unknown proteins. The algorithm consists of two stages: (i) a preprocessing stage…

Geomfinder
Web

Geomfinder

A web server for detailed estimation of similarities between all pairs of 3D…

A web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. Geomfinder is composed of four main steps: (i) generates on each…

lDDT
Web

lDDT local Distance Difference Test

A superposition-free score which evaluates local distance differences in a…

A superposition-free score which evaluates local distance differences in a model compared to a reference structure.

MCQ4Structures
Desktop

MCQ4Structures

Allows global comparison and research for small dissimilar fragments.…

Allows global comparison and research for small dissimilar fragments. MCQ4Structures applies mean of circular quantities (MCQ) for the purpose of structure similarity identification. It is based on…

AnEnPi
Web

AnEnPi Analogous Enzyme Pipeline

Assists user in the identification, clustering and annotation of analogous…

Assists user in the identification, clustering and annotation of analogous enzymes. AnEnPi is a web application that contains several features simplifying its utilization in different contexts. It…

MaxBench
Web

MaxBench

Assesses the ability of the sequence comparison methods in detecting sequence…

Assesses the ability of the sequence comparison methods in detecting sequence relationships and alignments quality. MaxBench is a web-based system available for evaluating the results of sequence and…

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