Protein structure prediction is the most important method in the area of developing science. It is also known as the holy grail of modern biology. It helps in the prediction of the three-dimensional structure of a protein from its amino acid sequence i.e. the prediction of its secondary, tertiary, and quaternary structure from its primary structure.

 

Tool Name

Description

 

MolSurfer:

A Macromolecular Interface Navigator. It is a Java-based program and can be used to study protein-protein and protein-DNA/RNA interfaces. The 2D projections of the computed interface aid visualization of complicated interfacial geometries in 3D.

 

InterPreTS prediction

It combines three-dimensional information of protein complexes, from their database of interacting domains, with an empirical scoring system to assess the fit of any potential protein interacting pair with a known three-dimensional structure. (Reference: P. Aloy & R.B. Russell (2003) Bioinformatics. 19, 161-162).

 

STRING

STRING stands for Search Tool for the Retrieval of Interacting Genes/Proteins. It is associated with high-throughput experimental data, mining databases and literature, and from predictions based on genomic context analysis. It assembles them in a common reference set, and presents evidence in a consistent and intuitive web interface. (Reference: C. von Mering et al. 2005. Nucleic Acids Research 33 (Database issue): D433-7).

YASPIN

It is built on three individual web servers: cons-PPISP, PINUP, and Promate. It is known as the meta web server and is used for protein-protein interaction and site prediction. (Reference: Qin, S.B. & Zhou, H.-X. 2007. Bioinformatics 23: 3386-3387)

JPred

Based upon PHD, Predator, DSC, NNSSP, Zpred and Mulpred programs It is a consensus method for protein secondary structure prediction. (European Bioinformatics Institute, Cambridge, United Kingdom).

TMpred

- Prediction of Trans-membrane Regions and Orientation - ISREC (Swiss Institute for Experimental Cancer Research)

TMHMM

Prediction of transmembrane helices in proteins (Center for Biological Sequence Analysis, The Technical University of Denmark)

DAS

Transmembrane Prediction Server (Stockholm University, Sweden)

SPLIT

Transmembrane Protein Topology Prediction Server provides modified hydrophobic moment index and clear, colorful output including beta reference

OCTOPUS

This tool uses a novel combination of hidden Markov models and artificial neural networks. It predicts the correct topology for 94% of the dataset of 124 sequences with known structures. (Reference: Viklund, H. & Elofsson, A. 2008. Bioinformatics 24: 1662-1668)

TMRPres2D

Stands for TransMembrane protein Re-Presentation in 2 Dimensions tool. It is a java based tool and takes data from a variety of protein folding servers and creates uniform, two-dimensional, high analysis graphical images/ models of alpha-helical or beta-barrel transmembrane proteins. (Reference: I.C. Spyropoulos et al. 2004. Bioinformatics 20: 3258-3260).

PRED-TMßß

Based on Hidden Markov Model method and is capable of predicting and discriminating beta-barrel outer membrane proteins. Gives one the opportunity to download a custom image plot or a 2D representation

TMB-Hunt

TransMembrane Barrel-Hunt and is based on amino acid composition. It provides with a color-coded score (& Evalue) for an individual or a series of proteins. (Reference: A.G. Garrow et al. 2005. Nucl. Acids Res. 33: W193-W197).

Coils

It helps in prediction of Coiled Coil Regions in Proteins (Swiss node of EMBnet, Switzerland) - (Reference: A. Lupas et al. 1991 Science 252: 1162-1164).

3D-PSSM

A Fast, Web-based Method for protein fold recognition. As an input it uses 1D and 3D sequence profiles coupled with secondary structure and solvation potential information. (Imperial Cancer Research Fund Fold Recognition Server)

PHYRE

Protein Homology/analogY Recognition Engine. It helps in the prediction of the 3D structure of proteins.

CPHModels

It consists of the following tools: Sowhat: A neural network based method to predict contacts between C-alpha atoms from the amino acid sequence. RedHom: A tool to find a subset with low sequence similarity in a database. Databases: Subsets of the Brookhaven Protein Data Bank (PDB) database with low sequence similarity produced using the RedHom tool. (Center for Biological Sequence Analysis, Technical University of Denmark)

SWISS-MODEL

An automated comparative protein modelling server. It require a viewer such as DeepView - Swiss-PdbViewer, Rasmol, Cn3D v3.0 or WebMol Java PDB. (Glaxo-Wellcome Experimental Research, Switzerland)

LOOPP

(Learning, Observing and Outputting Protein Patterns) A fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure. (Computational Biology Service Unit, Cornell Univ., U.S.A.).

3D-JIGSAW

Used in homology modelling. Save email results as *.pdb and view with Rasmol etc. (Biomolecular Modelling Laboratory, Cancer Research UK, England)

Protein Peeling:

An approach for splitting a 3D protein structure into compact fragments. (Reference: J.-C. Gelly et al. 2006. Bioinformatics 22: 129-133)

InterProSurf

It predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. (Reference: S.S. Negi et al. 2007. Bioinformatics. 23: 3397-3399).

ProtSkin

It converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP, MOLMOL or PyMOL.

GeNMR

(GEnerate NMR structure) - generates 3D protein structures using NOE-derived distance restraints and NMR chemical shifts. (Reference: M. Berjanskii et al. 2009. Nucl. Acids Res. 37(Web Server issue):W670-W677)