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Secondary structure prediction software tools | Protein structure data analysis

Protein secondary structure prediction (SSP) has been an area of intense research interest. Despite advances in recent methods conducted on large datasets, the estimated upper limit accuracy is yet to be reached. Since the predictions of SSP methods…
ANTHEPROT
Desktop

ANTHEPROT

Allows protein sequence analysis. ANTHEPROT is able to interactively couple…

Allows protein sequence analysis. ANTHEPROT is able to interactively couple multiple alignments with secondary structure predictions. It can submit tasks on a remote server and retrieve data from a…

ESPript
Web

ESPript Easy Sequencing in PostScript

Renders sequence similarities and secondary structure information for analysis…

Renders sequence similarities and secondary structure information for analysis and publication purposes. ESPript can assist users to optimize an alignment thank to its capability to display on the…

PSpro
Desktop

PSpro

Allows users to forecast protein secondary structure (SS). PSpro is also…

Allows users to forecast protein secondary structure (SS). PSpro is also efficient in predicting residue-residue contacts, contact map and solvent accessibility.

FELLS
Web
Desktop

FELLS Fast Estimator of Latent Local Structure

Aims to visualize structural features from the protein sequence. FELLS provides…

Aims to visualize structural features from the protein sequence. FELLS provides disorder, aggregation and low complexity predictions as well as estimated local propensities including amphipathicity.…

PCASSO
Web
Desktop

PCASSO Protein C-Alpha Secondary Structure Output

Assigns protein secondary structure elements (SSEs). PCASSO is based on the…

Assigns protein secondary structure elements (SSEs). PCASSO is based on the well-known random forest (RF) approach. It can be used in network analysis through SSE clustering, high-throughput SSE…

MUPRED
Web

MUPRED

Allows prediction of the three-dimensional structure of a protein. MUPRED uses…

Allows prediction of the three-dimensional structure of a protein. MUPRED uses both structural information and sequence profile information to realize this process. This tool first estimates the…

PHYSICO
Desktop

PHYSICO

Allows computation of properties of protein sequences. PHYSICO is an automated…

Allows computation of properties of protein sequences. PHYSICO is an automated standalone, multipurpose procedure for analysis of protein sequences. The software acts as position-based-substitution…

DNSS
Desktop

DNSS

Allows users to predict protein secondary structure (SS). DNSS supplies an ab…

Allows users to predict protein secondary structure (SS). DNSS supplies an ab initio method of deep learning network architectures which uses position specific scoring matrix of the protein sequence…

PDBparam
Web

PDBparam

Computes more than 50 structure-based features for any given protein structure.…

Computes more than 50 structure-based features for any given protein structure. PDBparam can deal with inter residue interactions, amino acid propensities, physicochemical properties, and binding…

STRIDE
Web
Desktop

STRIDE

Provides a software tool for secondary structure assignment from atomic…

Provides a software tool for secondary structure assignment from atomic resolution protein structures. STRIDE implements a knowledge-based algorithm that makes combined use of hydrogen bond energy…

Protein…
Web

Protein Beta-Sheet Structure Prediction

Predicts protein β-sheet structure. Protein Beta-Sheet Structure Prediction…

Predicts protein β-sheet structure. Protein Beta-Sheet Structure Prediction consist in a dynamic programing based algorithm for protein β-strands alignment. The software main features are (i)…

NetTurnP
Web

NetTurnP

Predicts two-class b-turns and the individual b-turn types. To proceed,…

Predicts two-class b-turns and the individual b-turn types. To proceed, NetTurnP uses evolutionary information and predicted protein sequence features. It was tested on a dataset of 426…

XRate
Desktop

XRate

Allows users to perform phylogenetic comparative genomics. Xrate is a package…

Allows users to perform phylogenetic comparative genomics. Xrate is a package that permits to provide maximum-likelihood analysis of multiple alignments and phylogenies using phylo-grammars as well…

conSSert
Web

conSSert Consensus Secondary Structure Prediction

A consensus secondary structure prediction method, based on support vector…

A consensus secondary structure prediction method, based on support vector machines (SVM) and providing exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a…

NIAS-Server
Web

NIAS-Server Neighbors Influence of Amino Acids and Secondary Structures

A server to help the analysis of the conformational preferences of amino acid…

A server to help the analysis of the conformational preferences of amino acid residues in proteins. NIAS is a web-based tool used to extract information about conformational preferences of amino acid…

BhairPred
Desktop
Web

BhairPred

Predicts beta-hairpins in a protein using the SVM approach. There are two…

Predicts beta-hairpins in a protein using the SVM approach. There are two options of sequence submission either directly paste in the text box or upload the file containing protein sequence.

DSSP
Dataset

DSSP

Standardizes secondary structure assignment. DSSP is a database of secondary…

Standardizes secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program…

PSIPRED
Web

PSIPRED Predict Secondary Structure

Aggregates a number of protein annotation tools and provides services or…

Aggregates a number of protein annotation tools and provides services or software to allow users to perform truly scalable biological analyses. PSIPRED offers to the user the possibility to choose…

PCI-SS
Web
PAGAL
Desktop

PAGAL

Calculates the hydrophobic moments of alpha helices (AHs). PAGAL can produce…

Calculates the hydrophobic moments of alpha helices (AHs). PAGAL can produce input files for a package allowing creation of high resolution graphics named TikZ. This input files permit users to…

EVA
Dataset

EVA

Aims to evaluate the accuracy of automated protein structure prediction…

Aims to evaluate the accuracy of automated protein structure prediction methods. EVA is updated automatically each week, to cope with the large number of existing prediction servers and the constant…

cleverSuite
Web

cleverSuite

Predicts secondary structure properties, solubility, chaperone requirements and…

Predicts secondary structure properties, solubility, chaperone requirements and RNA-binding abilities.

BetaTPred
Desktop
Web

BetaTPred

Predicts ß-turns in a protein from the amino acid sequence. It allows the user…

Predicts ß-turns in a protein from the amino acid sequence. It allows the user to predict turns in a protein using existing statistical algorithms, to predict the type of ß-turn such as Type I,…

KNIME-Extension…
Desktop

KNIME-Extensions

Provides a method to researchers in order to develop, validate, and deploy…

Provides a method to researchers in order to develop, validate, and deploy multi-step computational workflows. KNIME Extensions supplies a solution for scientists searching for a way to combine…

iCAPS
Web

iCAPS in silico comparative analysis of protein structures

Aims to help the user to compare a series of proteins in order to select a…

Aims to help the user to compare a series of proteins in order to select a target protein most suitable for initiation of protein engineering studies. iCAPS is a module of the iRDP Web Server that…

DEBT
Web

DEBT Dihedrally Enhanced Beta Turn prediction

Predicts both beta-turn location and beta-turn types (I, II, IV, VIII and NS).…

Predicts both beta-turn location and beta-turn types (I, II, IV, VIII and NS). DEBT is a web application that provides a simple interface. Users can paste or upload an archive or FASTA files to…

ASSP
Desktop
Web

ASSP Assignment of Secondary Structures in Proteins

Path traversed by the CA atoms is used to devise a new method, ASSP (Assignment…

Path traversed by the CA atoms is used to devise a new method, ASSP (Assignment of Secondary Structure in Proteins), for the identification of secondary structure elements in proteins. ASSP is an…

PreSSAPro
Web

PreSSAPro

Provides predictions of secondary structures starting from the amino acid…

Provides predictions of secondary structures starting from the amino acid sequence of a given protein. PreSSAPro uses the residue propensity values in different secondary structural types determined…

BCov
Desktop

BCov

An unsupervised method to predict the beta-sheet topology starting from the…

An unsupervised method to predict the beta-sheet topology starting from the protein sequence and its secondary structure. BCov takes advantage of the sparse inverse covariance estimation to define…

BetaTurns
Desktop
Web

BetaTurns

The prediction of beta-turns is an important element of protein secondary…

The prediction of beta-turns is an important element of protein secondary structure prediction. BetaTurns has been developed for the prediction of beta-turn types I, II, IV and VIII. For each turn…

PolyprOnline
Dataset

PolyprOnline

The polyproline helix type II (PPII) is a regular protein secondary structure…

The polyproline helix type II (PPII) is a regular protein secondary structure with remarkable features. Many studies have highlighted different crucial biological roles supported by this local…

AlphaPred
Web

AlphaPred

Predicts the alpha turn residues in the given protein sequence. The method is…

Predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary…

Betacon
Desktop

Betacon

Predicts beta-sheet topology in proteins.

Predicts beta-sheet topology in proteins.

garnier
Desktop

garnier

Predicts protein secondary structure using Garnier Osguthorpe Robson method.…

Predicts protein secondary structure using Garnier Osguthorpe Robson method. garnier reads an input protein sequence and writes a standard EMBOSS report file with the predicted secondary structure.…

SOPMA
Web

SOPMA Self-Optimized Prediction from Multiple Alignment

Predicts protein secondary structure by consensus prediction from multiple…

Predicts protein secondary structure by consensus prediction from multiple alignments. SOPMA correctly predicts 69.5% of amino acids for a three-state description of the secondary structure (a-helix.…

PSSpred
Web
Desktop

PSSpred Protein Secondary Structure PREDiction

A neural network training algorithm for accurate protein secondary structure…

A neural network training algorithm for accurate protein secondary structure prediction. PSSpred collects multiple sequence alignments using PSI-BLAST. Amino-acid frequence and log-odds data with…

Procalss
Web

Procalss

This server allows to predict the class of protein from its amino acid…

This server allows to predict the class of protein from its amino acid sequence. It predict weather protein belong to class Alpha or Beta or Alpha+Beta or Alpha/Beta.

APSSP2
Desktop
Web

APSSP2 Advanced Protein Secondary Structure Prediction

Predicts the secondary structure of proteins from their amino acid sequence.…

Predicts the secondary structure of proteins from their amino acid sequence. This is an advanced version of our PSSP server, which participated in CASP3 and in CASP4.

CDM
Web

CDM Consensus Data Mining

Provides secondary structure prediction algorithm. CDM is a hybrid method which…

Provides secondary structure prediction algorithm. CDM is a hybrid method which combines two structure prediction methods: Fragment Database Mining (FDM) and the GOR algorithm, GOR V. It enhances the…

norsp
Web

norsp

Predicts NO Regular Secondary structure (NORS) regions publicly accessible.…

Predicts NO Regular Secondary structure (NORS) regions publicly accessible. norsp extracts the secondary structure and evaluate the presence of transmembrane helices and coiled-coil in proteins. The…

DSSPcont
Web

DSSPcont

Recognizes conformational variations from a single X-ray structure and thereby…

Recognizes conformational variations from a single X-ray structure and thereby may assist predictions of functionally important residues. DSSPcont is able to distinguish well-defined from rigged…

LiveBench
Dataset

LiveBench

Is a continuously running benchmark project for assessing the quality of…

Is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods. LiveBench focuses mainly on homology modeling and…

PSSI
Desktop

PSSI probability-based protein secondary structure identification

Identifies protein secondary structure from NMR (nuclear magnetic resonance)…

Identifies protein secondary structure from NMR (nuclear magnetic resonance) chemical-shift data. Unlike the previously reported protocols, PSSI assigns the secondary structure type (β-strand,…

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