Protein Structure Prediction Software

The intricate dance of amino acids folding into functional proteins is a cornerstone of molecular biology. The constituent amino acids can be meticulously analyzed to predict the secondary, tertiary, and quaternary structures of proteins, offering profound insights into their biological roles and interactions. This article provides an exhaustive overview of notable software tools employed in protein structure prediction, encompassing homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.

Main Article: Protein Structure Prediction

Protein structure prediction is a critical field in computational biology, aiming to determine the three-dimensional structure of proteins from their amino acid sequences. This endeavor is pivotal for understanding protein function, interactions, and designing therapeutic interventions.

Software List

The following sections categorize software tools based on the methodologies they employ for structure prediction.

Homology Modeling

Homology modeling, also known as comparative modeling, leverages the structural information of known proteins to predict the structure of a target protein with a similar sequence.

Name	Method	Description	Release Date
IntFOLD	Unified Interface	A comprehensive platform for tertiary structure prediction, 3D modeling, model quality assessment, intrinsic disorder prediction, domain prediction, and prediction of protein-ligand binding residues.	Automated webserver and some downloadable programs
RaptorX	Remote Homology Detection	Specializes in remote homology detection, protein 3D modeling, and binding site prediction.	Automated webserver and Downloadable program
Biskit	Workflow Automation	Wraps external programs into automated workflows, including BLAST search, T-Coffee alignment, and MODELLER construction.	N/A
ESyPred3D	Template Detection	Focuses on template detection, alignment, and 3D modeling.	Automated webserver
FoldX	Energy Calculations	Performs energy calculations and protein design.	Downloadable program
Phyre , Phyre2	Remote Template Detection	Utilizes remote template detection, alignment, 3D modeling, multi-templates, and ab initio methods.	Webserver with job manager, automatically updated fold library, genome searching and other facilities
HHpred	Template Detection	Engages in template detection, alignment, and 3D modeling.	Interactive webserver with help facility
MODELLER	Spatial Restraints	Satisfies spatial restraints using a standalone program mainly in Fortran and Python.	Standalone program
CONFOLD	Contact and Distance Restraints	Satisfies contact and distance restraints using a standalone program mainly in Fortran and Perl.	Standalone program
Molecular Operating Environment (MOE)	Template Identification	Identifies templates, uses multiple templates, and accounts for other environments such as excluded ligand volumes.	Proprietary platform, supported on Windows, Linux and Mac
Robetta	Rosetta Homology Modeling	Employs Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction.	Webserver
BHAGEERATH-H	Ab Initio and Homology Methods	Combines ab initio folding and homology methods for protein tertiary structure predictions.	N/A
Swiss-model	Local Similarity	Uses local similarity and fragment assembly.	Automated webserver (based on ProModII)
Yasara	Template Detection	Detects templates, performs alignment, and models including ligands and oligomers.	Graphical interface or text mode (clusters)
AWSEM-Suite	Molecular Dynamics Simulation	Utilizes molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes.	Automated webserver

Threading and Fold Recognition

Protein threading, also known as fold recognition, is a method used to predict the structure of a protein by aligning its sequence with known protein structures.

Name	Method	Description	Release Date
IntFOLD	Unified Interface	A comprehensive platform for tertiary structure prediction, 3D modeling, model quality assessment, intrinsic disorder prediction, domain prediction, and prediction of protein-ligand binding residues.	Automated webserver and some downloadable programs
RaptorX	Remote Template Detection	Specializes in remote template detection, single-template and multi-template threading.	Webserver with job manager, automatically updated fold library
HHpred	Template Detection	Engages in template detection, alignment, and 3D modeling.	Interactive webserver with help facility
Phyre , Phyre2	Remote Template Detection	Utilizes remote template detection, alignment, 3D modeling, multi-templates, and ab initio methods.	Webserver with job manager, automatically updated fold library, genome searching and other facilities
I-TASSER	Threading Fragment Structure Reassembly	Employs threading fragment structure reassembly.	On-line server for protein modeling

Ab Initio Structure Prediction

Ab initio methods predict protein structures from scratch, without relying on known structures, using physical principles and computational algorithms.

Name	Method	Description	Release Date
trRosetta	Deep Learning	An algorithm for fast and accurate protein structure prediction, supporting single-sequence structure prediction with trRosettaX-Single.	Webserver and source codes available
ROBETTA	Rosetta Homology Modeling	Employs Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction.	Webserver
Rosetta@home	Distributed Computing	Implements the Rosetta algorithm through distributed computing.	Downloadable program
Abalone	Molecular Dynamics Folding	Uses molecular dynamics folding.	Program
C-QUARK	Deep Learning	A method for ab initio protein structure prediction based on deep-learning based contact-map predictions into the fragment assembly simulations.	Webserver
AlphaFold2	Deep Learning	An end-to-end deep learning framework for protein structure prediction.	Webserver and downloadable program
D-I-TASSER	Deep Learning	The deep learning-based I-TASSER program reportedly outperforms both AlphaFold2 and AlphaFold3.	Webserver

Secondary Structure Prediction

Secondary structure prediction focuses on identifying the local folding patterns of proteins, such as alpha helices and beta sheets.

For a detailed list of programs, refer to the List of protein secondary structure prediction programs .

External Links

bio.tools , finding more tools

List Of Protein Structure Prediction Software