Summary of Protein 3D Structure Prediction Software

Homology Modeling	Software	Method	Description
	AWSEM-Suite	Molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes	Automated webserver
	BHAGEERA TH-H	Combination of ab initio folding and homology methods	Protein tertiary structure predictions
	Biskit	Wraps external programs into an automated workflow	BLAST search, T-Coffee alignment, and MODE LLER construction
	CONFOLD	Satisfaction of contact and distance restraints	The standalone program mainly in Fortran and Perl
	ESyPred 3D	Template detection, alignment, 3D modeling	Automated webserver
	FoldX	Energy calculations and protein design	Downloadable programs
	HHpred	Template detection, alignment, 3D modeling	Interactive webserver with help facility
	IntFOLD	A unified interface for Tertiary structure prediction/3D modeling, 3D models quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues	Automated web server and some downloadable programs
	MODELLER	Satisfaction of spatial restraints	The standalone program mainly in Fortran and Python
	MOE	Template identification, use of multiple templates and accounting for other environments (e.g., excluded ligand volumes), loop modeling, rotamer libraries for sidechain conformations, and relaxation using MM forcefields.	Proprietary platform, supported on Windows, Linux, and Mac
	Phyre and Phyre2	Remote template detection, alignment, 3D modeling, multi-templates, ab initio	Webserver with job manager, automatically updated fold library, genome searching and other facilities
	RaptorX	Remote homology detection, protein 3D modeling, binding site prediction	Automated web server and downloadable programs
	Robetta	Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction	Webserver
	SWISS-MODEL	Local similarity/fragment assembly	Automated web server (based on ProModll)
	Yasara	Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments	Graphical interface or text mode (clusters)
Threading/Fold Recognition	IntFOLD	A unified interface for Tertiary structure prediction/3D modeling, 3D models quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues	Automated web server and some downloadable programs
	I-TASSER	Threading fragment structure reassembly	Online server for protein modeling
	Phyre and Phyre2	Remote template detection, alignment, 3D modeling, multi-templates, ab initio	Webserver with job manager, automatically updated fold library, genome searching and other facilities
	RaptorX	Remote template detection, single-template and multi-template threading, totally different from and much better than the old program RAPTOR designed by the same group	Webserver with job manager, automatically updated fold library
Ab initio Structure Prediction	Abalone	Molecular dynamics folding	Program
	C-QUARK	C-QUARK is a method for ab initio protein structure prediction. Based on deep learning-based contact-map predictions into the fragment assembly simulations.	Webserver
	Robetta	Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction	Webserver
	Robetta@home	Distributed-computing implementation of Rosetta algorithm	Downloadable program
	trRosetta	trRosetta is an algorithm for fast and accurate de novo protein structure prediction. It builds the protein structure based on direct energy minimizations with a restrained Rosetta. The restraints include inter-residue distance and orientation distributions, predicted by a deep residual neural network	Webserver and source codes. It takes about one hour to fold proteins with 300 AAs

Creative Biostructure has been working in the field of structural biology, membrane protein technologies, and structure-based drug discovery. We have expertise and experience in protein 3D structure prediction, protein modeling, and data analysis. Feel free to discuss your research project with our experts.

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