PEDANT: Protein Extraction, Description, and Analysis Tool

The PEDANT Genome Database contains automatically generated annotation of nearly 500 genomes by a variety of bioinformatics methods. Extensive graphical user interface, multiple functional and structural categories, detailed gene reports, DNA and Protein viewers, genome comparison.

PubMed Pedant Genome Database

PubMed Pedant software


MPPI: The MIPS Mammalian Protein–Protein Interaction database

Manually curated high-quality PPI data collected from the scientific literature by expert curators.

PubMed MPPI Database


DIMA:  Domain Interaction MAP

Prediction of interacting protein domains based on several computational methods as well as on experimental data.

PubMed The original DIMA method

PubMed The DIMA database

 

 

 


ISOBASE: A database of isochore information for all completely sequenced vertebrate genomes

Isochore assignments are made by several established techniques as well as by a consensus method. Confidence scores are also provided. Manuscript in preparation.


PROMPT: Protein Mapping Tool

Automate standard tasks in comparative proteomics. PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features.

PubMed PROMPT software


CAMPS: Computational Analysis of the Membrane Protein Space

A database of alpha-helical membrane protein families obtained by sequence clustering at three hierarchical levels: fold, function, and modeling distance.

PubMed CAMPS database


HelixCorr: predict interacting transmembrane helices

HelixCorr is a software to predict correlated mutations specifically for the transmembrane parts of membrane proteins. It includes predictions obtained by several individual prediction algorithms and combines them to a consensus prediction.

PubMed Method description


TMHcon: predict contacts for transmembrane proteins

Neural network based predictor for helix-helix contacts in alpha-helical membrane proteins.

PubMed Method description


Expropriator: Experimental Property Predictor of Proteins

Currently contains three independent methods to predict experimental behaviour of proteins listed below.

MemEx: Predict the amenability of membrane proteins to cloning, expression, and solubilization

PubMed Method description


PROSO: PROtein SOlubility

Predict solubility of globular proteins

PubMed Method description


SECRET: A Sequence-based CRystallizability EvaluaTor

A sequence-based approach to classify proteins into crystallizable and noncrystallizable

PubMed Method description


STRIDE: STRucture in DEfinition

Software for secondary structure assignment in proteins from known atomic coordinates plus a database of STRIDE assignments for all PDB structures

PubMed The original STRIDE method

PubMed The STRIDE server and database

 

 

 


ORPHEUS: Gene prediction in prokaryotic genomes

PubMed Method description

Download the ORPHEUS software

 

 

 


PREDATOR: protein secondary structure prediction

PubMed Method description