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Fold recognition software tools | Protein structure data analysis

Recognizing the correct structural fold among known template protein structures for a target protein (i.e. fold recognition) is essential for template-based protein structure modeling. Since the fold recognition problem can be defined as a binary…
RaptorX
Desktop
Web

RaptorX

A protein structure prediction server excelling at predicting 3D structures for…

A protein structure prediction server excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its…

HMMER
Desktop
Web

HMMER

Provides access to the protein homology search algorithms found in the HMMER…

Provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the…

PFP-Pred
Web

PFP-Pred

Predicts the fold of a protein. PFP-Pred consists of nine basic individual…

Predicts the fold of a protein. PFP-Pred consists of nine basic individual classifiers. It obtains an overall success rate of 62 per cent for a testing dataset where most of the proteins have more…

TM-fold
Web
Desktop

TM-fold

Is designed for automated protein structure classifications. For a given pair…

Is designed for automated protein structure classifications. For a given pair of protein structures, TM-fold calculates the structural similarity by structural alignment algorithms, and reports a…

DescFold
Web

DescFold Descriptor-based Fold Recognition System

Permits remote homology identification. DescFold relies on a support vector…

Permits remote homology identification. DescFold relies on a support vector machine-learning algorithm. It shows reasonable performance in any category, although its relative rankings change slightly…

EigenTHREADER
Desktop

EigenTHREADER

Enables fold recognition in instances where no homologous structures can be…

Enables fold recognition in instances where no homologous structures can be identified. EigenTHREADER takes a query amino acid sequence, generates a map of intra-residue contacts, and then searches a…

PFP-FunDSeqE
Web

PFP-FunDSeqE Protein Fold Prediction FUNctional Domain SEQuential Evolution

Predicts protein fold pattern. PFP-FunDSeqE fuses functional domain information…

Predicts protein fold pattern. PFP-FunDSeqE fuses functional domain information and sequential evolution information. It was tested on a set of proteins and was able to achieve over 70 per cent…

FFAS
Web
Desktop

FFAS Fold and Function Assignment System

Detects homology. FFAS includes adding optimized structural features…

Detects homology. FFAS includes adding optimized structural features (experimental or predicted), ‘symmetrical’ Z-score calculation and re-ranking the templates with a neural network. It has high…

FORTE
Web

FORTE

Allows protein fold recognition. FORTE is a fold recognition server based on a…

Allows protein fold recognition. FORTE is a fold recognition server based on a profile–profile comparison method. The software uses position-specific score matrices (PSSMs) of both query and…

SeqKernel
Desktop

SeqKernel

Allows users to solve the fold recognition problem. SeqKernel combines the…

Allows users to solve the fold recognition problem. SeqKernel combines the benefits of local string kernels using a substitution matrix and of the weighted degree kernels. This method allows…

GREMLIN
Web

GREMLIN Generative REgularized ModeLs of proteINs

A method to learn an undirected probabilistic graphical model of the amino acid…

A method to learn an undirected probabilistic graphical model of the amino acid composition within the multiple sequence alignments. GREMLIN employs regularization to penalize complex models and thus…

PFRES
Desktop

PFRES

Adopts a carefully designed, ensemble-based classifier. PFRES is a novel fold…

Adopts a carefully designed, ensemble-based classifier. PFRES is a novel fold classification method that uses a protein sequence representation, which consists of a small set of 36 features, and…

proFold
Web

proFold

A web server for protein fold classification. proFold is an ensemble classifier…

A web server for protein fold classification. proFold is an ensemble classifier combining the protein structural and functional information. proFold uses a feature extraction method combining the…

AGAPE
Desktop

AGAPE

Recognizes remote structural homologs in the PDB database. AGAPE can be applied…

Recognizes remote structural homologs in the PDB database. AGAPE can be applied to pairs of proteins with different sequences and similar structures considerably without ever using the information of…

SFoldRate
Web

SFoldRate

Predicts the folding rates for proteins of diverse classes based only on the…

Predicts the folding rates for proteins of diverse classes based only on the amino acid sequence of the protein. SFoldRate works even when protein sequences are based on alphabets of only two residue…

K-Fold
Web

K-Fold

A tool for the automatic prediction of the protein folding kinetic order and…

A tool for the automatic prediction of the protein folding kinetic order and rate.

HMMFold
Desktop

HMMFold

Extracts n-gram feature groups from the Hidden Markov Model (HMM)-profile to…

Extracts n-gram feature groups from the Hidden Markov Model (HMM)-profile to solve the Protein Fold Recognition (PFR). HMMFold is based on extracting evolutionary information from HMM pro- files. It…

DeepFR
Web

DeepFR

Predicts fold-specific features from predicted contacts for fold recognition.…

Predicts fold-specific features from predicted contacts for fold recognition. DeepFR is based on deep learning techniques. It employs deep convolutional neural network (DCNN) technique to identify…

SSKDSP
Desktop

SSKDSP Single-Source K Diverse Shortest Path

Approximates the top k shortest paths from the source to all other nodes in the…

Approximates the top k shortest paths from the source to all other nodes in the graph. SSKDSP is applicable to larger graphs. It can identify protein similarity between the query and each protein in…

Cofactory
Web
Desktop

Cofactory

Predicts enzyme cofactor specificity using only primary amino acid sequence…

Predicts enzyme cofactor specificity using only primary amino acid sequence information. Cofactory identifies potential cofactor binding Rossmann folds and predicts the specificity for the cofactors…

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…

LOMETS
Web

LOMETS Local Meta-Threading-Server

A local threading meta-server, for quick and automated predictions of protein…

A local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. LOMETS generates 3D models by collecting high-scoring target-to-template…

FoRSA
Web

FoRSA Fold Recognition using a Structural Alphabet

A unique fold recognition algorithm which is based on calculation of…

A unique fold recognition algorithm which is based on calculation of conditional probability for the amino acid sequence of a protein to fit to a particular fold. We use a structural alphabet, known…

PconsFold
Desktop

PconsFold

A fully automated pipeline for ab initio protein structure prediction based on…

A fully automated pipeline for ab initio protein structure prediction based on evolutionary information. PconsFold is based on PconsC contact prediction and uses the Rosetta folding protocol. Due to…

SeqRate
Web

SeqRate

Sequence-Based Protein Folding Rate Prediction Using Support Vector Machines.

Sequence-Based Protein Folding Rate Prediction Using Support Vector Machines.

ModLink+
Web

ModLink+

Uses both sequence similarity and protein–protein interactions to assign a…

Uses both sequence similarity and protein–protein interactions to assign a Structural Classification Of Proteins (SCOP) fold and a family classification to uncharacterized proteins. ModLink+ also…

SSThread
Desktop

SSThread

A template-free protein structure prediction program. SSThread predicts the…

A template-free protein structure prediction program. SSThread predicts the structure of contacting pairs of α-helices and β-strands that are derived from experimental structures followed by the…

DN-Fold
Web

DN-Fold

A deep learning network method to predict if a given query-template protein…

A deep learning network method to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features…

FOLDpro
Web

FOLDpro

A two-stage machine learning, information retrieval, approach to fold…

A two-stage machine learning, information retrieval, approach to fold recognition. First, we use alignment methods to derive pairwise similarity features for query-template protein pairs. We also use…

SPARKS-X
Web

SPARKS-X

A fold recognition server. SPARKS-X improves the single-method fold recognition…

A fold recognition server. SPARKS-X improves the single-method fold recognition technique called SPARKS by changing the alignment scoring function and incorporating the SPINE-X techniques that make…

PROSPECT
Desktop
Web

PROSPECT PROtein Structure Prediction and Evaluation Computer Toolkit

A threading-based protein structure prediction system. PROSPECT is designed…

A threading-based protein structure prediction system. PROSPECT is designed particularly for the recognition of the fold template whose sequence has insignificant homology to the target sequence. The…

Swfoldrate
Web

Swfoldrate

Predicting folding rates of proteins with sliding window.

Predicting folding rates of proteins with sliding window.

RF-Fold
Web

RF-Fold

A random forest method to recognize protein folds. RF-Fold was systematically…

A random forest method to recognize protein folds. RF-Fold was systematically validated by varying the input features and the class distribution of training datasets on a standard fold recognition…

SEGMER
Web

SEGMER

A segmental threading algorithm designed to recognizing substructure motifs…

A segmental threading algorithm designed to recognizing substructure motifs from the Protein Data Bank (PDB) library. SEGMER first splits target sequences into segments which consists of 2-4…

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…

FUGUE
Desktop
Web

FUGUE

A program for recognizing distant homologues by sequence-structure comparison.…

A program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid…

QUARK
Web

QUARK

A computer algorithm for ab initio protein folding and protein structure…

A computer algorithm for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only. QUARK models are built from…

MUSTER
Desktop
Web

MUSTER MUlti-Sources ThreadER

A protein threading algorithm to identify the template structures from the PDB…

A protein threading algorithm to identify the template structures from the PDB library. MUSTER generates sequence-template alignments by combining sequence profile-profile alignment with multiple…

SCOPE
Desktop

SCOPE Semi Classical Open Source Protein Energy

Allows users to recreate structures and explore the calculated non-bonded…

Allows users to recreate structures and explore the calculated non-bonded energy. SCOPE is a program utilizing the topology information to calculate Van der Waals energy and electrostatic energy of…

RPFOLD
Web

RPFOLD Protein Fold Recognition

A fold recognition server for searching protein fold in PDB. It is based on…

A fold recognition server for searching protein fold in PDB. It is based on sequence similarity search and secondary structure alignment technique.

Pred-PFR
Web

Pred-PFR Predicting Protein Folding Rate

Prediction of protein folding rates from primary sequence by fusing multiple…

Prediction of protein folding rates from primary sequence by fusing multiple sequential features.

PRORATE
Web

PRORATE

An approach to predict the folding rates for two-state and multi-state protein…

An approach to predict the folding rates for two-state and multi-state protein folders based on support vector regression (SVR).

FOLD-RATE
Web

FOLD-RATE

Predicts protein folding rates from amino acid sequence. FOLD-RATE is a method…

Predicts protein folding rates from amino acid sequence. FOLD-RATE is a method based on multiple regression technique. Different regression equations have been developed for proteins belonging to…

KineticDB
Dataset

KineticDB

Provides information about diverse data on protein folding kinetics. KineticDB…

Provides information about diverse data on protein folding kinetics. KineticDB is a relational database that contains single-domain proteins, and separates protein domains and short peptides without…

CATHEDRAL
Web

CATHEDRAL

An iterative protocol for determining the location of previously observed…

An iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure–based…

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