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Contact map detection software tools | Protein structure data analysis

Protein residue–residue contact prediction is the problem of predicting whether any two residues in a protein sequence are spatially close to each other in the folded 3D structure. Contacts occurring between sequentially distant residues, i.e.…
PconsC
Desktop
Web

PconsC

Identifies protein-like contact patterns to improve contact predictions. PconsC…

Identifies protein-like contact patterns to improve contact predictions. PconsC is a random forest (RF) approach that uses predictions from two methods of inferring direct information: PSICOV…

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.

PSICOV
Desktop

PSICOV

Introduces the use of sparse inverse covariance estimation to the problem of…

Introduces the use of sparse inverse covariance estimation to the problem of protein contact prediction. PSICOV displays a mean precision substantially better than the best performing normalized…

ACE
Desktop

ACE Adaptive Cluster Expansion

Infers quickly and accurately Ising or Potts models based on correlation data.…

Infers quickly and accurately Ising or Potts models based on correlation data. ACE avoids overfitting by constructing a sparse network of interactions sufficient to reproduce the observed correlation…

3D Complex
Dataset

3D Complex

A hierarchical classification of protein complexes that describes similarities…

A hierarchical classification of protein complexes that describes similarities in structure, sequence, as well as topology of contacts of the constituent proteins.

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…

AAindex
Dataset

AAindex Amino-Acid Index

A database of numerical indices representing various physicochemical and…

A database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections: AAindex1 for the amino…

CoinFold
Web

CoinFold

A web server for ab initio protein contact and tertiary structure prediction…

A web server for ab initio protein contact and tertiary structure prediction without using any templates. In particular, CoinFold predicts contacts by joint evolutionary coupling (EC) analysis via…

ConKit
Desktop

ConKit

Allows facile conversion between formats and provides an interface to analyse…

Allows facile conversion between formats and provides an interface to analyse sequence alignments and sets of contact predictions. ConKit permits to handle and manipulate residue-residue contact…

DeepConPred
Desktop

DeepConPred

Improves the prediction of long-range residue-residue contacts. DeepConPred…

Improves the prediction of long-range residue-residue contacts. DeepConPred integrates two deep learning models in a hierarchical strategy. It predicts the coarse contact information between two…

RRCRank
Algorithm

RRCRank

Provides a method to detect protein residue-residue contact by using a ranking…

Provides a method to detect protein residue-residue contact by using a ranking strategy. RRCRank uses correlated mutations methods and ensemble machine-learning classifiers to predict contact…

COUSCOus
Desktop

COUSCOus Contact predictiOn Using Shrinked COvariance

A residue-residue contact detecting method approaching contact inference in a…

A residue-residue contact detecting method approaching contact inference in a similar manner as PSICOV, by applying the sparse inverse covariance estimation technique. COUSCOus combines the best…

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…

direct_contact_…
Desktop

direct_contact_prediction

Analyzes large scale co-fractionation / mass spectrometry (CF-MS) datasets.…

Analyzes large scale co-fractionation / mass spectrometry (CF-MS) datasets. direct_contact_prediction consists in an orthogonal approach that determines aspects of the three-dimensional architecture…

FreeContact
Desktop

FreeContact

Provides the opportunity to compute reliable contact predictions in any…

Provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). FreeContact is a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of…

RBO Aleph
Web

RBO Aleph

A protein structure prediction web server for template-based modeling, protein…

A protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein…

BCL
Desktop

BCL BioChemical Library

Provides a set of tools for biological research. BCL can be used to determine…

Provides a set of tools for biological research. BCL can be used to determine protein structure from sparse experimental data. It contains programs that are able to assemble secondary structure…

KScons
Algorithm

KScons

A Bayesian statistical model using knob-socket information that maximizes…

A Bayesian statistical model using knob-socket information that maximizes contact prediction accuracy from a combination of priors and posteriors. The resulting program was then compared over 3…

R2C
Web

R2C Residue-Residue contact

A residue-residue contact predictor that combines machine learning-based and…

A residue-residue contact predictor that combines machine learning-based and correlated mutation analysis-based methods, together with a two-dimensional Gaussian noise filter to enhance the…

XLmap
Desktop

XLmap

Integrates cross-linked site information with protein contact maps. XLmap…

Integrates cross-linked site information with protein contact maps. XLmap evaluates the overlap between the cross-linking information with the protein contact map over a specified distance range…

RaptorX…
Web

RaptorX Contact Prediction

Allows contact prediction and contact-assisted protein folding. RaptorX Contact…

Allows contact prediction and contact-assisted protein folding. RaptorX Contact Prediction is a deep learning method for contact prediction. The software uses a combination of two deep residual…

CCMpred
Desktop

CCMpred

A fast GPU and CPU implementation of a top-performing pseudo-likelihood…

A fast GPU and CPU implementation of a top-performing pseudo-likelihood maximization (PLM)-based contact prediction approach that runs in a fraction of the time of comparably accurate methods. The…

PROTMAP2D
Desktop

PROTMAP2D

Analyzes contact maps. PROTMAP2D aims to ease comparative analysis of protein…

Analyzes contact maps. PROTMAP2D aims to ease comparative analysis of protein structures, mainly in case which the mutual position and interactions of residues have to been take into account. The…

RDb2C
Desktop

RDb2C Ridge-Detection-based β-β Contact predictor

Allows users to predict β-β contact. RDb2C proposes an approach based on…

Allows users to predict β-β contact. RDb2C proposes an approach based on ridge detection for improving the detection at both residue and strand level from predicted contact maps. The software first…

DCA forecasting
Desktop

DCA forecasting

Forecasts the accuracy of residue-residue contact predictions for individual…

Forecasts the accuracy of residue-residue contact predictions for individual proteins. DCA forecasting is a method which could be employed to predict gplmDCA and PSICOV. This model could be helpful…

COLORS
Web

COLORS improving COntact prediction using LOw-Rank and Sparse matrix decomposition

Permits to remove background correlations. COLORS is based on the low-rank and…

Permits to remove background correlations. COLORS is based on the low-rank and sparse matrix decomposition (LRS) technique. It can differentiate true correlations from background correlations…

NeBcon
Desktop

NeBcon

Uses the Bayes classifier (NBC) theorem to combine eight state of the art…

Uses the Bayes classifier (NBC) theorem to combine eight state of the art contact methods that are built from co-evolution and machine learning approaches. NeBcon (Neural-network and Bayes-classifier…

STING Contacts
Web

STING Contacts

Identifies and visualizes amino acid contacts within protein structure and…

Identifies and visualizes amino acid contacts within protein structure and across protein interfaces. STING Contacts calculates atomic contacts among amino acids based on a table of predefined pairs…

bbcontacts
Desktop

bbcontacts

A Python program predicting residue-level contacts between beta-strands by…

A Python program predicting residue-level contacts between beta-strands by detecting patterns in matrices of predicted couplings. bbcontacts can make use of a secondary structure assignment or a…

RRDistMaps
Desktop

RRDistMaps

Contact maps are a convenient method for the structural biologist to identify…

Contact maps are a convenient method for the structural biologist to identify structural features through two-dimensional simplification. Binary (yes/no) contact maps with a single cutoff distance…

MemConP
Desktop

MemConP Membrane Contact Prediction

A contact prediction method for α-helical transmembrane proteins, in which…

A contact prediction method for α-helical transmembrane proteins, in which evolutionary couplings are combined with a machine learning approach. MemConP achieves a substantially improved accuracy…

NNcon
Desktop

NNcon

A fast and reliable web server and software for protein contact map prediction.…

A fast and reliable web server and software for protein contact map prediction. NNcon was ranked among the most accurate methods in the CASP8 experiment, 2008. The contact map predicted by NNcon can…

CMPyMOL
Desktop

CMPyMOL

An add-on software to molecular visualization program PyMOL. CMPyMOL combines…

An add-on software to molecular visualization program PyMOL. CMPyMOL combines the protein 3D visualization capabilities of PyMOL and the protein's 2D contact map with an interactive interface…

pyMDmix
Desktop

pyMDmix python Molecular Dynamics simulations with mixed solvents

Identifies high affinity interaction spots over macromolecular systems by means…

Identifies high affinity interaction spots over macromolecular systems by means of molecular dynamics simulations using solvent mixtures as solvation conditions. pyMDMix is a python module and a user…

CONFOLD
Web

CONFOLD

An ab initio protein folding method to build three-dimensional models using…

An ab initio protein folding method to build three-dimensional models using predicted contacts and secondary structures. Our method first translates contacts and secondary structures into distance,…

BND
Desktop
Web

BND

A balanced network deconvolution algorithm to identify optimized dependency…

A balanced network deconvolution algorithm to identify optimized dependency matrix without limit on the eigenvalue range in the applied network systems. The algorithm was used to filter contact…

EPC-map
Desktop
Web

EPC-map Evolutionary and Physicochemical information to predict Contact maps

A contact prediction method that achieves unprecedented prediction accuracy by…

A contact prediction method that achieves unprecedented prediction accuracy by combining evolutionary information from multiple-sequence alignments with physicochemical information from structure…

plmDCA
Desktop

plmDCA pseudolikelihood maximization Direct-Coupling Analysis

Separates direct from indirect interactions in the context of protein…

Separates direct from indirect interactions in the context of protein sequences. plmDCA was applied to 21-state Potts models describing the statistical properties of families of evolutionarily…

PROFisis
Web

PROFisis

Identifies interacting residues from sequence alone. PROFisis is a…

Identifies interacting residues from sequence alone. PROFisis is a computational-method that reliably identifies interface residues from sequence could, therefore, be extremely valuable. It…

SVM-SEQ
Desktop
Web

SVM-SEQ

An algorithm for protein residue-residue contact prediction. SVM-SEQ generates…

An algorithm for protein residue-residue contact prediction. SVM-SEQ generates the predictions only based on sequence information, where secondary structures, solvent accessibility, sequence profile…

FT-COMAR
Desktop

FT-COMAR Fault Tolerant Contact Map Reconstruction

A heuristic algorithm for the reconstruction of the protein three-dimensional…

A heuristic algorithm for the reconstruction of the protein three-dimensional structure from (possibly) incomplete (i.e. containing unknown entries) and noisy contact maps. FT-COMAR runs within…

PROFcon
Desktop

PROFcon

A contact prediction method that combines information from alignments, from…

A contact prediction method that combines information from alignments, from predictions of secondary structure and solvent accessibility, from the region between two residues and from the average…

CMAPpro
Web

CMAPpro

A machine learning approach for contact map prediction using three steps of…

A machine learning approach for contact map prediction using three steps of increasing resolution. For long-range contacts, the accuracy of the CMAPpro predictor is close to 30%, a significant…

CMView
Desktop

CMView

Integrates rich contact map analysis with 3D visualization using PyMol. CMView…

Integrates rich contact map analysis with 3D visualization using PyMol. CMView provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space…

DNCON
Web

DNCON

A method for protein residue–residue prediction. The approach is based on two…

A method for protein residue–residue prediction. The approach is based on two concepts, boosted ensembles and deep networks (DNs), which are novel in the context of residue–residue contact…

PhyCMAP
Web

PhyCMAP

A method for contact map prediction, integrating both evolutionary and physical…

A method for contact map prediction, integrating both evolutionary and physical restraints by machine learning and integer linear programming. The evolutionary restraints are much more informative…

PSP server
Web

PSP server

Contains a collection of web services that address several protein structure…

Contains a collection of web services that address several protein structure prediction (PSP) sub-problems. Each of these sub-problems focuses on a single structural feature of a protein and the PSP…

CNNcon
Algorithm

CNNcon

An improved multiple neural networks based contact map predictor using six…

An improved multiple neural networks based contact map predictor using six sub-networks and one final cascade-network. The method performs better on prediction accuracy than other compared…

C2S
Desktop
Web

C2S Contact Map-to-Structure

An automated procedure for building full atom protein structures based on…

An automated procedure for building full atom protein structures based on contact maps. C2S can be used to reconstruct monomeric and multimeric proteins. C2S is a three-step procedure which uses…

Distill
Web

Distill

A suite of servers for the prediction of protein structural features: secondary…

A suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8…

SVMcon
Web

SVMcon

A contact map predictor that uses SVMs and a large set of informative features.…

A contact map predictor that uses SVMs and a large set of informative features. SVMcon yields good performance on medium- to long-range contact predictions and can be modularly incorporated into a…

DCA
Web

DCA Direct-Coupling Analysis

A computationally implementation of direct-coupling analysis (DCA), which…

A computationally implementation of direct-coupling analysis (DCA), which allows to evaluate the accuracy of contact prediction by DCA for a large number of protein domains. DCA is shown to yield a…

EPSILON-CP
Web

EPSILON-CP

Allows contact prediction. EPSILON-CP combines evolutionary information from…

Allows contact prediction. EPSILON-CP combines evolutionary information from multiple sequence alignments with physicochemical information from structure prediction methods and with sequence-based…

MetaPSICOV
Web

MetaPSICOV

Combines three distinct approaches for inferring covariation signals from…

Combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics…

ConEVA
Web
Desktop

ConEVA Protein Contact Evaluation

Allows protein contact evaluation and comparison. ConEVA allows a user to…

Allows protein contact evaluation and comparison. ConEVA allows a user to choose from various contact types, distance thresholds, and sequence separation thresholds for defining contacts and enables…

CMWeb
Web

CMWeb Contact Map Web Viewer

An online tool for studying basic properties of residue-residue contact…

An online tool for studying basic properties of residue-residue contact formation and contact clusters. CMWeb can be used for inspecting proteins only with 3D structure, for visualizing contact maps,…

ProC_S3
Web

ProC_S3

A set of Random Forest algorithm based models, for predicting residue–residue…

A set of Random Forest algorithm based models, for predicting residue–residue contact maps. ProC_S3 is based on a collection of 1490 non–redundant, high-resolution protein structures using…

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