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.
MPPI: The MIPS Mammalian Protein–Protein Interaction database
Manually curated high-quality PPI data collected from the scientific literature by expert curators.
DIMA: Domain Interaction MAP
Prediction of interacting protein domains based on several computational methods as well as on experimental data.
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.
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.
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.
TMHcon: predict contacts for transmembrane proteins
Neural network based predictor for helix-helix contacts in alpha-helical membrane proteins.
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
SECRET: A Sequence-based CRystallizability EvaluaTor
A sequence-based approach to classify proteins into crystallizable and noncrystallizable
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
PREDATOR: protein secondary structure prediction
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.