Wednesday, June 13, 2007

2d structure predictions tools


3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

Bioinformatics Toolkit -

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.


Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.


The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

CBS DAS protein viewer

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.


Prediction of coiled coil regions.

ConPred II

ConPred II is a tool for predicting transmembrane topology for a user-supplied query sequence. Results are presented in a variety of forms including hydropathy plots.


A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.


A computational tool for prediction of disordered/unstructured regions within a protein sequence.


DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.


ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.


EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

IBM Bioinformatics and Pattern Discovery Group

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.


iMolTalk is a set of tools for protein structure analysis. Users have access to tools to extract information from PDB files, create Ramachandran plots or alpha-carbon distance matrices, align two structures or a sequence to a structure, search for contacts for a residue, and identify the interface between chains.

Institute of Enzymology Servers

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.


Java Protein Dossier (JPD) is part of the STING Suite of web based programs for visualization and analyses of molecular structures. JPD can display many different physicochemical parameters for PDB files as well as for structurally aligned pairs of PDB files.


NORSp (predictor of Non-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.


Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.


PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.


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