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Structure decoy creation software tools | Protein data analysis

Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields.Source text:(Deng et al., 2016) 3DRobot: automated generation of diverse and…
I-TASSER
Web
Desktop

I-TASSER Iterative Threading ASSEmbly Refinement

Allows automated protein structure prediction and structure-based function…

Allows automated protein structure prediction and structure-based function annotation. I-TASSER constructs, starting from the amino acid sequence, 3D structural models by reassembling fragments…

RW
Desktop

RW

Provides distance-dependent atomic potential for protein structure modeling and…

Provides distance-dependent atomic potential for protein structure modeling and structure decoy recognition. RW was derived from 1,383 high-resolution protein data bank (PDB) structures using an…

Decoyfinder
Desktop

Decoyfinder

Finds decoy molecules for a given target. Decoyfinder is an application…

Finds decoy molecules for a given target. Decoyfinder is an application designed to build target-specific decoy sets. The software selects decoys both :(i) similar to active ligands according to five…

MODELLER
Desktop

MODELLER

A software tool used for homology or comparative modeling of protein…

A software tool used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and…

3DRobot
Desktop
Web

3DRobot

A program devoted for automated generation of diverse and well-packed protein…

A program devoted for automated generation of diverse and well-packed protein structure decoys. Given a native structure as input, 3DRobot first identifies diverse structure scaffolds from a…

CABS-flex
Web

CABS-flex

An efficient procedure for the simulation of structure flexibility of folded…

An efficient procedure for the simulation of structure flexibility of folded globular proteins. Three consecutive steps follow the CABS simulation procedure: (i) structural clustering, (ii) models…

Decoys 'R' Us
Dataset

Decoys 'R' Us

Contains incorrect conformations to improve protein structure prediction. Decoy…

Contains incorrect conformations to improve protein structure prediction. Decoy ‘R’ Us provides a resource that allows scoring functions to be improved. It can be used to evaluate and improve…

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