Rita Casadio

Biocomputing Group Main Research Fields (http://www.biocomp.unibo.it)

• Protein sequence analysis
• Prediction of protein secondary structure and of membrane protein topology with machine learning approaches
• Protein folding prediction from aminoacid sequence: statistical potentials, contact maps for 3D structure prediction, distance geometry, recognition of nucleation sites, prediction of disulfide bridges with neural networks, prediction of the topology of membrane proteins, model building by homology, threading.
• Structural and functional annotation of proteomes
• Annotation of gene and protein variants
• Protein-protein and protein-nucleic acids interaction networks

Tools based on NN and NN/HMM in Bologna can predict:

• The secondary structure of proteins
• The initiation sites of protein folding
• The topology of all-alpha and all-beta membrane proteins (SGI Best Paper Award at ISMB 2002)
• The presence of signal peptides
• The bonding state of cysteines and the topology of disulfide bridges
• The contact map of proteins (Best performing predictor in the category at CASP4 and CASP5)
• The protein-protein interaction surfaces
• The protein stability upon mutation

Predictors developped by the Biocomputing Group

• BaCelLo - Balanced subCellular Localization predictor

• BAR+ - Bologna Annotation Resource

• BetAware - Detection of Prokaryotic outer-membrane betabarrel proteins

• CCHMM - Predictor of Coiled-Coils Regions in Proteins

• CCHMMPROF - Predictor of Coiled-Coils Regions in Proteins exploiting evolutionary information

• CORNET - Predictor of Residue Contacts in Proteins

• DCON - Predictor of Disulfide Connectivity in Proteins

• DisLocate - Find Disulfide bonds in Eukaryotes with predicted subcellular Localization

• FT-COMAR - Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps

• HIPPIE - Protease Inhibitor engine

• I-MUTANT - Neural Network based Predictor of Protein stability Changes upon Single Point Mutation from the Protein Structure

• I-MUTANT 2.0 - Support Vector Machines based Predictor of Protein stability Changes upon Single Point Mutation from the Protein Sequence and Structure

• I-MUTANT Suite - Support Vector Machines based Predictor of Protein stability Changes upon Single Point Mutation from the Protein Sequence and Structure (three states) and of human Deleterious Single Nucleotide Polymorphysms

• ISPRED - Predictor of Protein Interaction Sites

• K-Fold - Predictor of the Protein Folding Mechanism and Rate

      ·   MemLoci - Subcellular Localization Predictor for Membrane Proteins

• MemPype - A pipeline for predicting the topology and the localization of membrane proteins

• PhD-SNP - Support Vector Machines based Predictor of human Deleterious Single Nucleotide Polymorphysms

• PredGPI - Predictor of GPI-Anchored Proteins

• SNPs&GO - Predictor of Human Disease-related Mutations in Proteins with Functional Annotations

• SPEPLip - Predictor of Signal Peptide and Lipoprotein Cleavage Sites in Proteins

• YAP - Yet Another Alignment Program (Pairwise Sequence Alignment Using Secondary Structures)

• prototypes and old predictors

Application Servers

• TRAMPLE : the transmembrane protein labelling environment

• PONGO : a web server for multiple predictions of all-alpha transmembrane proteins

Databases

• eSLDB - eukaryotic Subcellular Localization DataBase

• ZenPatches - Database of predicted protein interaction sites

• DBMFHS - Data Base of Minimally-Frustrated Helical Segments