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Crystallization detection software tools | Protein structure data analysis

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial…
ProteinCCD
Web

ProteinCCD Protein Crystallisation Construct Designer

Helps deciding how to choose promising constructs for protein expression and…

Helps deciding how to choose promising constructs for protein expression and crystallisation. ProteinCCD functions as a meta-server that collects information from prediction servers concerning…

Crysf
Web

Crysf

Permits to select feasible target proteins from UniProt for structural…

Permits to select feasible target proteins from UniProt for structural determination. Crysf predicts crystallization propensities (CPs) based on user-submitted protein sequences of interest. It…

Crysalis
Web

Crysalis

An integrated crystallization analysis tool that builds on support-vector…

An integrated crystallization analysis tool that builds on support-vector regression (SVR) models to facilitate computational protein crystallization prediction, analysis, and design. More…

SCMMTP
Web

SCMMTP Scoring Card Method Membrane Transport Proteins

Identifies and characterizes membrane transport proteins (MTPs). SCMMTP uses…

Identifies and characterizes membrane transport proteins (MTPs). SCMMTP uses dipeptide composition as a feature for predicting and characterizing MTPs. It was tested on three datasets: a human…

TargetCrys
Web

TargetCrys

A sequence-based protein crystallization predictor by fusing multi-view protein…

A sequence-based protein crystallization predictor by fusing multi-view protein features with two-layered SVM (2L-SVM). TargetCrys was compared with existing sequence-based protein crystallization…

I-TASSER-MR
Web

I-TASSER-MR

Serves to resolve problem of distant-homology proteins in X-ray…

Serves to resolve problem of distant-homology proteins in X-ray crystallography. I-TASSER-MR produces full-length models working with I-TASSER by iterative structural fragment reassembly. Then, it…

ParCrys
Web

ParCrys

A Parzen Window approach to estimate a protein's propensity to produce…

A Parzen Window approach to estimate a protein's propensity to produce diffraction-quality crystals. The Protein Data Bank (PDB) provided training data whilst the databases TargetDB and PepcDB…

ContaBase
Dataset

ContaBase

A contaminant database to allow fast MR-based screening of crystallographic…

A contaminant database to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. ContaBase was compiled from publications, postings on the CCP4 Bulletin…

ContaMiner
Web
Desktop

ContaMiner

A rapid automated large-scale detection of contaminant crystals. ContaMiner…

A rapid automated large-scale detection of contaminant crystals. ContaMiner allows fast MR-based screening of crystallographic data against currently 62 known contaminants. It currently produces…

SVMCRYS
Desktop

SVMCRYS

Predicts protein crystallization propensity using sequence derived features.…

Predicts protein crystallization propensity using sequence derived features. SVMCRYS can classify proteins into ‘amenable to crystallization’ and ‘resistant to crystallization’. It accepts…

fDETECT
Desktop

fDETECT

Determines the eligibility of targets for crystallization. fDETECT investigates…

Determines the eligibility of targets for crystallization. fDETECT investigates crystallization propensity and the resulting coverage by X-ray structures of the current snapshot of the protein…

PredPPCrys
Web

PredPPCrys Prediction of Procedures Propensity for protein Crystallization

An accurate prediction of sequence clone, protein production, purification and…

An accurate prediction of sequence clone, protein production, purification and crystallization propensity from sequence by multi-step heterogeneous feature fusion and selection. PredPPCrys uses a…

PPCpred
Web

PPCpred

Predicts propensity for production of diffraction-quality crystals, production…

Predicts propensity for production of diffraction-quality crystals, production of crystals, purification and production of the protein material. PPCpred utilizes comprehensive set of inputs based on…

XtalPred
Web

XtalPred

A web server for prediction of protein crystallizability. The prediction is…

A web server for prediction of protein crystallizability. The prediction is made by comparing several features of the protein with distributions of these features in TargetDB and combining the…

OB-Score
Desktop

OB-Score

A Z-score scale to rank potential targets by their predicted propensity to…

A Z-score scale to rank potential targets by their predicted propensity to produce diffraction-quality crystals. The OB-Score is derived from a matrix of predicted isoelectric point and…

XANNpred
Web

XANNpred

A pair of artificial neural networks that each predict the propensity of a…

A pair of artificial neural networks that each predict the propensity of a selected protein sequence to produce diffraction-quality crystals by current structural biology techniques. On blind test…

SECRET
Web

SECRET SEquence-based CRystallizability EvaluaTor

A Web server for protein crystallizability prediction. SECRET is a…

A Web server for protein crystallizability prediction. SECRET is a machine-learning approach to sequence-based prediction of protein crystallizability in which we exploit subtle differences between…

CRYSTALP
Web

CRYSTALP

A kernel-based method that predicts the propensity of a given protein sequence…

A kernel-based method that predicts the propensity of a given protein sequence to produce diffraction-quality crystals. CRYSTALP2 utilizes the composition and collocation of amino acids, isoelectric…

PDPredictor
Web

PDPredictor

Proposes applications to analyze and provide optimal boundary information for…

Proposes applications to analyze and provide optimal boundary information for query sequences and to visualize the data. PDPredictor website hosts high-throughput structure determination pipelines…

cctbx
Desktop

cctbx Computational Crystallography Toolbox

Contains fundamental algorithms for computational crystallography that are…

Contains fundamental algorithms for computational crystallography that are designed for integration into highly automated software systems, but are also suitable for smaller systems, including…

CaspR
Web

CaspR

Reduces the need for expensive and time-consuming phasing experiments. CaspR…

Reduces the need for expensive and time-consuming phasing experiments. CaspR executes an optimized molecular replacement procedure using a combination of well-established stand-alone software tools.…

SCMCRYS
Desktop

SCMCRYS

An ensemble method for prediction of protein crystallization based on a scoring…

An ensemble method for prediction of protein crystallization based on a scoring card method (SCM) with the sequence features of p-collocated amino acid pairs. The SCM classifier determines the…

Crystal Studio
Desktop

Crystal Studio

Permits to create crystal structure with stunning color and 3D realism in just…

Permits to create crystal structure with stunning color and 3D realism in just a few mouse clicks. Crystal Studio is a multi-document and a multi-view integrated software. Empowered with a…

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