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Quality assessment software tools | Protein structure data analysis

Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is…
Qprob
Web
Desktop

Qprob

A single-model quality assessment (QA) method. Different from other…

A single-model quality assessment (QA) method. Different from other single-model QA methods, Qprob estimates the prediction error estimation of several different physicochemical, structural and…

RPF
Web

RPF Recall Precision F-measure

Validates ‘R-factor’-like protein structure. RPF calculates a…

Validates ‘R-factor’-like protein structure. RPF calculates a discriminating power (DP) score that estimates how well the query structure satisfies the data relative to a statistical random-coil…

VADAR
Web

VADAR Volume Area Dihedral Angle Reporter

Calculates, identifies, graphs, reports and/or evaluates a large number…

Calculates, identifies, graphs, reports and/or evaluates a large number (>30) of key structural parameters both for individual residues and for the entire protein. VADAR is a comprehensive web…

PSVS
Web

PSVS Protein Structure Validation Suite

Assesses protein structures generated by nuclear magnetic resonance (NMR) or…

Assesses protein structures generated by nuclear magnetic resonance (NMR) or X-ray crystallographic methods. PSVS provides standard constraint analyses, statistics on the PDB (protein data bank)…

PROSESS
Web

PROSESS Protein Structure Evaluation Suite & Server

Evaluates and validates protein structures solved by either X-ray…

Evaluates and validates protein structures solved by either X-ray crystallography or NMR (Nuclear magnetic resonance) spectroscopy. PROSESS integrates a variety of previously developed, well-known…

ProQ3D
Web
Desktop

ProQ3D

Predicts the quality of model structures based on a single model. ProQ3D is the…

Predicts the quality of model structures based on a single model. ProQ3D is the deep learning version of ProQ3 program. It employs both the structural information derived from the three-dimensional…

Harmony
Web

Harmony

Examines the compatibility between the sequence and the structure of a protein…

Examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local…

ResProx
Web

ResProx

Predicts the atomic resolution of nuclear magnetic resonance (NMR) protein…

Predicts the atomic resolution of nuclear magnetic resonance (NMR) protein structures. ResProx estimates, with a correlation coefficient of 0.92 between observed and calculated, the atomic resolution…

MQAPRank
Web
Desktop

MQAPRank Model Quality Assessment Program Rank

Assesses global protein model quality. MQAPRank is based on a learning-to-rank…

Assesses global protein model quality. MQAPRank is based on a learning-to-rank approach and uses single method to sort the decoy models. Models are classified by their similarities with the…

ProQM-resample
Desktop

ProQM-resample

Uses a support vector machine (SVM) to predict the quality of a membrane…

Uses a support vector machine (SVM) to predict the quality of a membrane protein model by combining structural and sequence-based features calculated from the model. ProQM-resample is a model quality…

GMQ
Desktop

GMQ Graph-based Model Quality assessment method

Predicts local quality of a structure model by considering quality of…

Predicts local quality of a structure model by considering quality of neighboring residues. GMQ uses conditional random field and performs a binary prediction of the quality of each residue in a…

SVMQA
Desktop

SVMQA

Predicts TM-score and GDT_TS score based on a feature vector containing…

Predicts TM-score and GDT_TS score based on a feature vector containing statistical potential energy terms and consistency-based terms between the actual structural features (extracted from the…

ModFOLD
Desktop

ModFOLD

A server which provides global and local prediction of the quality of 3D models…

A server which provides global and local prediction of the quality of 3D models of proteins. ModFOLD, is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single…

ProTSAV
Web

ProTSAV Protein Structure Analysis and Validation

Furnishes the user with a single quality score in case of individual protein…

Furnishes the user with a single quality score in case of individual protein structure along with a graphical representation and ranking in case of multiple protein structure assessment. ProTSAV is…

QMEAN
Web

QMEAN

A method for estimating the absolute quality of a single protein structure,…

A method for estimating the absolute quality of a single protein structure, i.e. without including additional information from other models or alternative template structures. QMEAN is based on the…

SELECTpro
Web
Desktop

SELECTpro

Selects effective protein model. SELECTpro combines high and low-resolution…

Selects effective protein model. SELECTpro combines high and low-resolution energy terms into a model selection method that is effective on model sets of variable size, diversity, and target…

ModFOLDclustQ
Desktop

ModFOLDclustQ

A novel Model Quality Assessment Program that compares 3D models of proteins…

A novel Model Quality Assessment Program that compares 3D models of proteins without the need for CPU intensive structural alignments by utilizing the Q measure for model comparisons. ModFOLDclust…

PconsD
Desktop

PconsD

A very fast method for blind estimation of the objective quality (similarity to…

A very fast method for blind estimation of the objective quality (similarity to the native structure) of predicted models of protein structures (model quality assessment). PconsD relies on stream…

ConQuass
Desktop
Web

ConQuass

A quality assessment program based on the consistency between the model…

A quality assessment program based on the consistency between the model structure and the protein’s conservation pattern. ConQuass can identify problematic structural models, and that the scores it…

MaxSub
Desktop

MaxSub

An automated measure for the assessment of protein structure prediction…

An automated measure for the assessment of protein structure prediction quality, that further builds and extends some of the evaluation methods introduced at CASP3. MaxSub aims at identifying the…

SMOQ
Desktop

SMOQ

A tool for protein single model quality assessment. SMOQ can predict the…

A tool for protein single model quality assessment. SMOQ can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines with protein sequence and…

RFMQA
Desktop

RFMQA Random Forest-Based Protein Model Quality Assessment

Estimates the relative quality of a set of model protein structures. RFMQA…

Estimates the relative quality of a set of model protein structures. RFMQA combines various scoring functions and consistency terms between predicted values and calculated values from 3D models. It…

ModelEvaluator
Desktop

ModelEvaluator

A machine learning model evaluation method to predict the quantitative absolute…

A machine learning model evaluation method to predict the quantitative absolute quality score of a single model using structural features extracted from its 3D coordinates and predicted from its…

GOBA
Desktop

GOBA Gene Ontology-Based Assessment

A protein model quality assessment program. GOBA estimates the compatibility…

A protein model quality assessment program. GOBA estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected…

ProQ
Web

ProQ

A model quality assessment algorithm that uses support vector machines to…

A model quality assessment algorithm that uses support vector machines to predict local as well as global quality of protein models. ProQ2 was developed to improve both local and global single-model…

BioLuminate
Desktop

BioLuminate

Provides a comprehensive modeling solution for biologics. BioLuminate is a user…

Provides a comprehensive modeling solution for biologics. BioLuminate is a user interface and the kynchpin product of the Biologics Suite that is designed from the ground up, with significant user…

FRST
Web
Desktop

FRST Function of RAPDF Solvation and Torsion potentials

Validates the energy of a protein structure. FRST combines four knowledge-based…

Validates the energy of a protein structure. FRST combines four knowledge-based potentials recognizing different features. It helps to produce native-like structures and is able to discriminate the…

Apollo
Desktop
Web

Apollo Assessing Protein single or multiple models

A web server to provide the community with access to all three model quality…

A web server to provide the community with access to all three model quality assessment approaches (i.e. single, clustering and hybrid). Apollo evaluates the absolute global and local qualities of a…

PROPKA
Web

PROPKA

Detects the pKa values for the ionizable residue. PROPKA is a web application,…

Detects the pKa values for the ionizable residue. PROPKA is a web application, based on an empirical method, that can be queried from a PDB ID, a PDB file or an URL. Predictions are particularly…

DeepQA
Desktop

DeepQA

A single-model quality assessment method based on deep belief network that…

A single-model quality assessment method based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy,…

VoroMQA
Web
Desktop

VoroMQA Voronoi tessellation-based Model Quality Assessment

Allows for the estimation of protein structure quality. VoroMQA combines the…

Allows for the estimation of protein structure quality. VoroMQA combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived…

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