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Multiple structure alignment software tools | Protein data analysis

Multiple protein structure alignment (MPStrA) is an important approach for functional and evolutionary analysis of groups of protein structures. Typically, MPStrA is used to identify the conserved regions that form the common structural core of a…
MAFFT
Web
Desktop

MAFFT

Allows alignment of multiple sequences. MAFFT provides a range of different…

Allows alignment of multiple sequences. MAFFT provides a range of different methods such as L-INS-I or FFT-NS-2. It permits to add unaligned sequences into an existing alignment. This tool can…

BAli-Phy
Desktop

BAli-Phy BAli-Phy

A Bayesian posterior sampler that employs Markov chain Monte Carlo to explore…

A Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward…

DIALIGN
Web

DIALIGN

A software tool for multiple sequence alignment by combining global and local…

A software tool for multiple sequence alignment by combining global and local alignment features. DIALIGN composes multiple alignments from local pairwise sequence similarities. This approach is…

Expresso
Web

Expresso

A multiple sequence alignment server that aligns sequences using structural…

A multiple sequence alignment server that aligns sequences using structural information. Providing the suitable structural information is available, Expresso delivers sequence alignments with…

BAliBASE
Dataset

BAliBASE

Provides high quality reference alignments based on 3D structural…

Provides high quality reference alignments based on 3D structural superpositions. BAliBASE is a large scale benchmarks specifically designed for multiple sequence alignment. The alignment test cases…

STRAP
Desktop

STRAP STRuctural Alignments of Proteins

A versatile workbench for protein analysis that can be used to generate and…

A versatile workbench for protein analysis that can be used to generate and refine multiple alignments, to download PDB files from public ftp servers, visualize protein structural data with plugin or…

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…

StatAlign
Desktop

StatAlign

Samples from the joint posterior distribution of phylogenies, alignments and…

Samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying the Markov chain Monte Carlo (MCMC) method. StatAlign also offers tools for efficient…

PyMod
Desktop

PyMod

Acts as simple and intuitive interface between PyMOL and several bioinformatics…

Acts as simple and intuitive interface between PyMOL and several bioinformatics tools (i.e., PSI-BLAST, Clustal Omega, MUSCLE, CAMPO, PSIPRED, and MODELLER). PyMod builds homology models through the…

FSA
Web

FSA Fast Statistical Alignment

A program for the alignment of multiple biological sequences that is both…

A program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice.

MUSTANG
Desktop

MUSTANG MUltiple STructural AligNment AlGorithm

A package which reports the multiple sequence alignment and the corresponding…

A package which reports the multiple sequence alignment and the corresponding superposition of structures. MUSTANG aligns residues on the basis of similarity in patterns of both residue-residue…

MAMMOTH-mult
Web

MAMMOTH-mult

It multiply aligns protein structures, providing a common 3D superimposition, a…

It multiply aligns protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.

Matt
Web

Matt Multiple Alignment with Translations and Twists

An aligned fragment pair chaining algorithm that, in intermediate steps, allows…

An aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments.

PSSweb
Web

PSSweb Protein Structural Statistics web server

A web server for protein structural statistics. PSSweb takes as input an…

A web server for protein structural statistics. PSSweb takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for…

Opal
Desktop

Opal

A package for aligning multiple biological sequences. Opal attains accuracy on…

A package for aligning multiple biological sequences. Opal attains accuracy on par with the state-of-the-art without altering the alignment scoring function by increasing gap penalties near…

MASS
Desktop
Web

MASS Multiple Alignment by Secondary Structures

An efficient method for multiple alignment of protein structures and detection…

An efficient method for multiple alignment of protein structures and detection of structural motifs.

SALIGN
Web

SALIGN

Versatile protein multiple sequence/structure alignment module of MODELLER.

Versatile protein multiple sequence/structure alignment module of MODELLER.

Vorolign
Web

Vorolign

A fast and flexible structural alignment method for two or more protein…

A fast and flexible structural alignment method for two or more protein structures.

OXBench
Dataset

OXBench

Includes data and software to evaluate the accuracy of protein multiple…

Includes data and software to evaluate the accuracy of protein multiple sequence alignments.

Theseus
Desktop

Theseus

A program that simultaneously superimposes multiple macromolecular structures.

A program that simultaneously superimposes multiple macromolecular structures.

M-Coffee
Web

M-Coffee

Uses consistency to estimate a consensus alignment. M-Coffee is an extension of…

Uses consistency to estimate a consensus alignment. M-Coffee is an extension of T-Coffee and a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several…

MUMMALS
Web

MUMMALS MUltiple alignment with Multiple MAtch state models of Local Structure

Improves alignment quality by using pairwise alignment hidden Markov models…

Improves alignment quality by using pairwise alignment hidden Markov models (HMMs) with multiple match states that describe local structural information without exploiting explicit structure…

MODELLER
Desktop

MODELLER

A software tool used for homology or comparative modeling of protein…

A software tool used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and…

POSA
Web

POSA Partial Order Structure Alignment

A method of multiple protein structure alignment developed using a partial…

A method of multiple protein structure alignment developed using a partial order graph representation of multiple alignments.

MISTRAL
Web

MISTRAL Multiple STRuctural Alignment

A strategy for multiple protein alignment based on the minimization of an…

A strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules.

MMLigner
Web
Desktop

MMLigner

Infers statistically significant structural alignments. MLigner can also…

Infers statistically significant structural alignments. MLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes.…

QuanTest
Desktop

QuanTest

Represents a powerful and flexible way to test multiple sequence alignment…

Represents a powerful and flexible way to test multiple sequence alignment (MSA) quality where the alignments are being used to detect or demonstrate homology or for structure prediction. QuanTest is…

TFcompare
Web

TFcompare

Superposes pairs of transcription factor (TF)-DNA complexes in order to obtain…

Superposes pairs of transcription factor (TF)-DNA complexes in order to obtain structural alignments of cis elements recognized by homologous TFs. TFcompare calculates structural alignments between…

Superpose3D
Desktop

Superpose3D

Allows local structural comparison. Superpose3D allows users to flexibly…

Allows local structural comparison. Superpose3D allows users to flexibly specify the way that residues are to be represented during the computation and the pairing rules. The software also allows…

mulPBA
Web

mulPBA

This server implements a method based on a structural alphabet to describe the…

This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles.

PsychoProt
Web
Desktop

PsychoProt Physical CHemistry Of Protein variability

A web app and a package to study about protein modeling, evolution and design.…

A web app and a package to study about protein modeling, evolution and design. PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are…

MS3ALIGN
Web
Desktop

MS3ALIGN Multi-Scale Morse-Smale Molecular-Surface Alignment tool

Aligns molecular surfaces based on significant protrusions on the molecular…

Aligns molecular surfaces based on significant protrusions on the molecular surface. A key advantage of MS3ALIGN is robust segmentation of the surface into segments that can be individually evaluated…

PSAlign
Desktop

PSAlign

A multiple sequence alignment program that finds a multiple alignment of k…

A multiple sequence alignment program that finds a multiple alignment of k sequences which preserves k-1 pairwise alignments as specified by edges of a given tree in polynomial time without using a…

PDBeFold
Web

PDBeFold

Allows to compare protein structures in 3D. PDBeFold is the European…

Allows to compare protein structures in 3D. PDBeFold is the European Bioinformatics Institute-Macromolecular Structure Database (EBI-MSD) web service Secondary Structure Matching (SSM). The software,…

Kalign
Web

Kalign

Improves both the accuracy and speed of multiple sequence alignment by…

Improves both the accuracy and speed of multiple sequence alignment by employing the Wu-Manber string-matching algorithm. Kalign follows a strategy analogous to the standard progressive method for…

FASMA
Web

FASMA Formatting and Analysing the Sequences in the Multiple Alignments

Analyzes and provides customized visualization of multiple sequence alignments.…

Analyzes and provides customized visualization of multiple sequence alignments. FASMA allows users to compare and analyze the aligned sequences, including for investigate conservation in specific…

PCMA
Desktop

PCMA Profile Consistency Multiple sequence Alignment

Applies the fast algorithm of ClustalW to align highly similar sequences and…

Applies the fast algorithm of ClustalW to align highly similar sequences and the T-Coffee algorithm to align the relatively divergent pre-aligned groups. PCMA is a progressive multiple sequence…

PDBpaint
Web

PDBpaint

A visualization tool for designing prediction structure from raw sequences of…

A visualization tool for designing prediction structure from raw sequences of proteins. PDBpaint can compute predicted features from the sequence extracted and locally run methods: protein domains by…

3DCOMB
Desktop

3DCOMB

A package to generate a multiple structure alignment (MSA) with not only as…

A package to generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments. 3DCOMB is unique in that it makes use of both…

SiteBinder
Web

SiteBinder

Allows for the multiple superimposition of large sets of protein structural…

Allows for the multiple superimposition of large sets of protein structural motifs. SiteBinder performs a systematic search for the atom pairing that provides the best fit. During this search, the…

SARpred
Desktop
Web

SARpred

A neural network based method predicts the real value of surface accessibility…

A neural network based method predicts the real value of surface accessibility (SA) by using multiple sequence alignment. In this method, two feed forward, back-propagation networks are used. The…

MultiProt
Desktop
Web

MultiProt

Detects structural motifs shared only by a subset of the molecules. MultiProt…

Detects structural motifs shared only by a subset of the molecules. MultiProt provides a web app and an application that aim to solve the multiple structural alignment problem with detection of…

StralSV
Web

StralSV Structure Alignment-based Sequence Variability

Implements a structure-based algorithm for identifying and aligning structure…

Implements a structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue…

msTALI
Desktop
Web

msTALI

A multiple structure alignment algorithm that utilizes several types of…

A multiple structure alignment algorithm that utilizes several types of information, including torsion angles, backbone atom positions, surface accessibility, residue type, and others.

RNAsalsa
Desktop

RNAsalsa

Adapts known structure information to the considered sequences in several…

Adapts known structure information to the considered sequences in several steps. RNAsalsa uses structure information for adjusting and refining the sequence alignment and vice versa. Conserved…

pepwindowall
Desktop

pepwindowall

Draws Kyte-Doolittle hydropathy plot for a protein alignment. pepwindowall…

Draws Kyte-Doolittle hydropathy plot for a protein alignment. pepwindowall calculates hydropathy in windows of a specified size over the input sequences. Users can provide their own data files in…

CE-MC
Web

CE-MC

Provides a web-based facility for the alignment of multiple protein structures…

Provides a web-based facility for the alignment of multiple protein structures based on C-alpha coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods.

HOMSTRAD
Dataset

HOMSTRAD HOMologous STRucture Alignment Database

Allows study of both sequence and structure relationships between homologous…

Allows study of both sequence and structure relationships between homologous proteins. HOMSTRAD is a database that provides combined protein sequence and structure information extracted from the…

3dLOGO
Web

3dLOGO

A web server for the identification and analysis of conserved protein 3D…

A web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in…

SABERTOOTH
Web

SABERTOOTH

Performs protein structure alignments by using the protein structure.…

Performs protein structure alignments by using the protein structure. SABERTOOTH allows to analyze structure-to-structure, structure-to-sequence and sequence-to-sequence alignments in the same…

Smolign
Web

Smolign

Spatial motifs based multiple protein structure alignment.

Spatial motifs based multiple protein structure alignment.

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