Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Pairwise structure alignment software tools | Protein data analysis

It is well known that conservation of proteins at the structure level can be much higher than at the sequence level (Holm and Sander, 1996). Recognizing similarities in protein structures and classifying them into folds, families, etc. is therefore…
FATCAT
Web
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…

ProBis
Web

ProBis Protein Binding Sites

Helps for prediction and study of protein binding sites and their ligands.…

Helps for prediction and study of protein binding sites and their ligands. ProBiS provides algorithm, database, and web servers based on graph theoretical approaches combined with molecular…

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…

TM-align
Web

TM-align

A highly optimized algorithm for protein structure comparison and alignment.

A highly optimized algorithm for protein structure comparison and alignment.

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…

LGA
Web

LGA Local-Global Alignment

A Method for Finding 3D Similarities in Protein Structures.

A Method for Finding 3D Similarities in Protein Structures.

Kpax
Desktop

Kpax

A fast protein structure alignment and database search program. Kpax uses…

A fast protein structure alignment and database search program. Kpax uses Gaussian functions to score very rapidly the local and spatial environment of each amino acid residue in a protein, and it…

TM-Score
Web
Desktop

TM-Score

Provides a metric for measuring the structural similarity of two protein…

Provides a metric for measuring the structural similarity of two protein models. Template modeling score (TM-Score) is designed to solve two major problems in the traditional metrics such as…

TopMatch
Web
Desktop

TopMatch

Allows to align and superpose a pair of protein structures. TopMatch is a…

Allows to align and superpose a pair of protein structures. TopMatch is a structure-matching technique which integrates established structure-matching techniques with appropriate techniques for the…

CLICK
Web
Desktop

CLICK

Aligns the 3D structures of any pair of biomolecules, independent of topology.…

Aligns the 3D structures of any pair of biomolecules, independent of topology. CLICK is an algorithm that provides 3D structures by matching cliques of points. It consists of four sequential steps:…

SMS
Web

SMS STING Millennium Suite

Provides a variety of algorithms and validated data, wrapped-up in a user…

Provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing…

ProCKSI
Web

ProCKSI Protein (Structure) Comparison, Knowledge, Similarity and Information

Allows protein structure comparison. ProCKSI is a decision support system that…

Allows protein structure comparison. ProCKSI is a decision support system that facilitates protein structural comparison by allowing the user to compare multiple protein structures seamlessly using…

T-DB
Dataset

T-DB TOPOFIT-DB

A public web-based database of protein structural alignments based on the…

A public web-based database of protein structural alignments based on the TOPOFIT method, providing a comprehensive resource for comparative analysis of protein structure families.

VAST
Web

VAST Vector Alignment Search Tool

A computer algorithm developed at NCBI and used to identify similar protein…

A computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by…

ALADYN
Web

ALADYN

Aligns pairs of protein structures by comparing their internal dynamics and…

Aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements.

FAST
Web
Desktop

FAST Fast Alignment and Search Tool

Aligns 3D structures of proteins. FAST is a clustering-based algorithm that…

Aligns 3D structures of proteins. FAST is a clustering-based algorithm that employs various techniques to eliminate incompatible residue-pairs and reduce computational complexity. The software…

SCALI
Web

SCALI Structural Core ALIgnment

It can efficiently find conserved packing arrangements, even if they are…

It can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space.

Fr-TM-align
Desktop

Fr-TM-align

A program for protein structural alignment. Fr-TM-align employs fragment…

A program for protein structural alignment. Fr-TM-align employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The structural alignments generated…

GANGSTA+
Web

GANGSTA+

A combinatorial algorithm for non-sequential structural alignment of proteins…

A combinatorial algorithm for non-sequential structural alignment of proteins and similarity search in databases. Since GANGSTA+ ignores the polypeptide chain connectivity of SSEs (secondary…

MatAlign
Desktop

MatAlign Matrix Alignment

A software used to compare 3D protein structures, based on the alignment of…

A software used to compare 3D protein structures, based on the alignment of distance matrices. The 3D protein structure is represented as 2D distance matrices and aligned, then the initial alignment…

SHEBA
Desktop

SHEBA Structural Homology by Environment-Based Alignment

An initial alignment is made by comparing a one-dimensional list of primary,…

An initial alignment is made by comparing a one-dimensional list of primary, secondary and tertiary structural features (profiles) of two proteins, without explicitly considering the…

SPalign
Desktop
Web

SPalign

Optimizes SP-score for structure alignment. SPalign was applied to recognize…

Optimizes SP-score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding. For fold discrimination,…

LovoAlign
Desktop
Web

LovoAlign

The methods used for structural alignment are based on Low Order Value…

The methods used for structural alignment are based on Low Order Value Optimization (LOVO) theory.

ProBiS-Database
Dataset

ProBiS-Database

A repository for structurally similar protein binding sites analysis of the…

A repository for structurally similar protein binding sites analysis of the proteins of known structures in the Protein Data Bank (PDB).

TOPS++FATCAT
Web

TOPS++FATCAT

Fast flexible structural alignment using constraints derived from TOPS+ strings…

Fast flexible structural alignment using constraints derived from TOPS+ strings models.

SSEalign
Web

SSEalign Secondary Structure Element alignment

Allows homology identification of hypothetical proteins. SSEalign is a…

Allows homology identification of hypothetical proteins. SSEalign is a web-server that can be useful for re-annotating proteins with unknown functions, especially for the bacterial proteins.

UniAlign
Web

UniAlign

A protein pairwise structure alignment algorithm that incorporates additional…

A protein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles and residue conservation.…

PROSTA
Desktop

PROSTA PROtein STructure Alignment tools

Automatically determines and aligns the interaction interfaces between two…

Automatically determines and aligns the interaction interfaces between two arbitrary types of complex structures, e.g. protein–protein complexes, protein–DNA complexes and protein–RNA…

DeepAlign
Web
Desktop

DeepAlign

A method for automatic pairwise protein structure alignment.

A method for automatic pairwise protein structure alignment.

DEDAL
Desktop

DEDAL

A protein structure alignment tool which is independent of rigid-body…

A protein structure alignment tool which is independent of rigid-body constraints.

MM-align
Desktop
Web

MM-align

An algorithm for structurally aligning multiple-chain protein-protein…

An algorithm for structurally aligning multiple-chain protein-protein complexes. MM-align is built on a heuristic iteration of a modified Needleman-Wunsch dynamic programming (DP) algorithm, with the…

CSA
Web

CSA Comparative Structural Alignment

A webserver for computing and comparing protein structure alignments. CSA exact…

A webserver for computing and comparing protein structure alignments. CSA exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the…

CAB-Align
Desktop

CAB-Align Contact Area-Based Alignment

A protein structure alignment method which uses the residue-residue contact…

A protein structure alignment method which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the…

SCPC
Web
Desktop

SCPC Structural Comparison of Protein Complexes

Makes comparisons between protein complexes. SCPC analyzes the structure of two…

Makes comparisons between protein complexes. SCPC analyzes the structure of two protein complexes employing secondary structure elements (SSEs). SCPC divides complexes into subunits and scores…

iAlign
Desktop
Web

iAlign interface Alignment

An interface alignment method for the structural alignment of protein-protein…

An interface alignment method for the structural alignment of protein-protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming…

SAS-Pro
Desktop

SAS-Pro

Provides an optimal structural alignment between any given pair of proteins.

Provides an optimal structural alignment between any given pair of proteins.

CTSS
Desktop

CTSS

A tool for protein structure alignment. CTSS takes 2 protein structures as…

A tool for protein structure alignment. CTSS takes 2 protein structures as input and computes shape signatures as curvature and torsion values along the Calpha virtual backbone. The location in the…

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…

Matchprot
Desktop

Matchprot

A package for protein structure comparison scheme. Matchprot is capable of…

A package for protein structure comparison scheme. Matchprot is capable of detecting correct alignments even in difficult cases. The program calculates correct alignments for proteins with huge…

partiFold-Align
Web

partiFold-Align

Uses dynamic programming schemes to simultaneously list the complete space of…

Uses dynamic programming schemes to simultaneously list the complete space of structures and sequence alignments and compute the optimal solution. PartiFold-Align is an algorithm for simultaneous…

ASH
Web

ASH Alignment of Structural Homologs

Provides a structural alignment program. ASH, based on a double dynamic…

Provides a structural alignment program. ASH, based on a double dynamic programming algorithm, intends to maximize the number of structurally equivalent residues between two proteins. The application…

MAFFTash
Web

MAFFTash

Allows users to compute multiple sequence alignments (MSA). MAFFTash is a web…

Allows users to compute multiple sequence alignments (MSA). MAFFTash is a web application that authorizes to perform sequences and structures through two software in a row. First, inputs are…

LMSfit
Desktop

LMSfit

Overlaps two protein conformations by their atomic coordinates using a robust…

Overlaps two protein conformations by their atomic coordinates using a robust statistics technique: least median of squares (LMS). LMSfit can automatically detect and superimpose the rigid core…

MICAN
Desktop

MICAN

A protein structure alignment algorithm. MICAN is a structure alignment…

A protein structure alignment algorithm. MICAN is a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, Calpha only models, Alternative…

GASH
Web
Desktop

GASH Genetic algorithm ASH

Computes globally optimal alignment. GASH can estimate the true maximum of the…

Computes globally optimal alignment. GASH can estimate the true maximum of the Number of Equivalent Residues (NER) score for an arbitrary pair of protein structures. It is based on a double dynamic…

TOPS+
Web

TOPS+

Allows protein structure comparison. TOPS+ is a comparison method for novel…

Allows protein structure comparison. TOPS+ is a comparison method for novel topological models that uses parameter optimization both for the computation of the dynamic programming table and the…

MolLoc
Web

MolLoc Molecular Local surface comparison

A web server for the structural comparison of molecular surfaces. Given two…

A web server for the structural comparison of molecular surfaces. Given two structures in PDB format, the user can compare their binding sites, cavities or any arbitrary residue selection. Moreover,…

SPalignNS
Web
Desktop

SPalignNS

A non-sequential protein structure alignment tool by using a novel asymmetric…

A non-sequential protein structure alignment tool by using a novel asymmetric linear sum assignment heuristic. Specifically, the Asymmetric Greedy Search algorithm was shown to produce viable…

MAX-PAIRS
Desktop

MAX-PAIRS

A polynomial time algorithm for finding a near-optimal superposition of two…

A polynomial time algorithm for finding a near-optimal superposition of two proteins.

Consensus
Web

Consensus

Produces high-quality alignments for comparative modeling, and identifies the…

Produces high-quality alignments for comparative modeling, and identifies the alignment regions reliable for copying from a given template. Consensus produces a consensus alignment, with a…

TALI
Web

TALI Torsion angle ALIgnment

Performs local structural constraint based on torsion angles rather than other…

Performs local structural constraint based on torsion angles rather than other local or global structural constraints. TALI provides a structural alignment method which utilizes local structural…

ALIGN_MTX
Web

ALIGN_MTX

Makes pairwise alignment for different types of substitution matrices such as…

Makes pairwise alignment for different types of substitution matrices such as evolutionary change-based substitution matrices (ECBSM), threading matrices, or position-specific score matrices (PSSM).…

PROPOSAL
Desktop

PROPOSAL PROtein comparison through Probabilistic Optimal Structure local Alignment

A Gibbs sampling algorithm for multiple local alignments of 3D protein…

A Gibbs sampling algorithm for multiple local alignments of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.