Data Mining Protein Structures' Topological Properties to Enhance Contact Map Predictions

Data Mining Protein Structures' Topological Properties to Enhance Contact Map Predictions Dr. Jaume Bacardit School of Computer Science and School of Biosciences University of Nottingham [email_address] Weizmann Institute of Sciences, May 27 th , 2010

Preface ,[object Object],[object Object],[object Object],[object Object]

Roadmap ,[object Object],[object Object],[object Object],[object Object],[object Object],PSP  TP  CM  CASP  INS

PROTEIN STRUCTURE AND CONTACT MAP PREDICTION PSP  TP  CM  CASP  INS

Protein Structure Prediction ,[object Object],Primary Sequence 3D Structure

Why PSP? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

PSP: A family of problems ,[object Object],[object Object],[object Object],[object Object],[object Object]

PSP sub-problems ,[object Object],[object Object],[object Object],[object Object],[object Object]

TOPOLOGICAL PROPERTIES OF PROTEINS PSP  TP  CM  CASP  INS

Contact Map ,[object Object],[object Object],[object Object],[object Object],Contact helices sheets

Recursive Convex Hull ,[object Object],[object Object],[object Object],[object Object],[object Object]

Recursive Convex Hull ,[object Object]

Relation of RCH to other structural properties ,[object Object],[object Object],[object Object],[object Object],[object Object]

Proximity Graphs (PGs) DT ⊇ GG ⊇ RNG ⊇ MST Poupon: 2004 Delanuy Tessellation of a point set ,[object Object]

Proximity Graphs (PGs) DT ⊇ GG ⊇ RNG ⊇ MST ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Residue Packing Density ,[object Object],[object Object],Contact Map Public calculation server: http://lobelia.cs.nott.ac.uk/psp/newInterface/

Predictability of RCH ,[object Object],[object Object],[object Object],[object Object],[object Object]

Predictability of RCH ,[object Object]

Is RCH more predictable than other features? ,[object Object]

But is it useful? ,[object Object],[object Object]

OUR CONTACT MAP PREDICTION METHOD PSP  TP  CM  CASP  INS

Steps ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Using BioHEL [Bacardit et al., 09]

The BioHEL GBML System ,[object Object],[object Object],[object Object],[object Object],[object Object]

Iterative Rule Learning ,[object Object]

Characteristics of BioHEL ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Prediction of RCH, SA and CN ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

How are these features predicted? ,[object Object],[object Object],R i SS i R i+1 SS i+1 R i-1 SS i-1 R i+2 SS i+2 R i-2 SS i-2 R i+3 SS i+3 R i+4 SS i+4 R i-3 SS i-3 R i-4 SS i-4 R i-5 SS i-5 R i+5 SS i+5 R i-1 R i R i+1  SS i R i R i+1 R i+2  SS i+1 R i+1 R i+2 R i+3  SS i+2

Prediction of RCH, SA and CN ,[object Object],[object Object],[object Object],[object Object]

Characterisation of the contact map problem ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],1 2 3

1. Three windows of residues ,[object Object],[object Object],[object Object],[object Object],[object Object]

Description of connecting segment and the whole sequence ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Contact Map dataset ,[object Object],[object Object],[object Object],[object Object],[object Object]

Samples and ensembles ,[object Object],[object Object],[object Object],[object Object],[object Object],Training set x50 x25 Consensus Predictions Samples Rule sets

CONTACT MAP PREDICTION AT CASP9 PSP  TP  CM  CASP  INS

Contact Map prediction in CASP ,[object Object],[object Object],[object Object],[object Object]

Accuracy Results ,[object Object],Ezkudia et al. Proteins 2009; 77(Suppl 9):196-209

Xd results Ezkudia et al. Proteins 2009; 77(Suppl 9):196-209

[object Object],[object Object],Ezkudia et al. Proteins 2009; 77(Suppl 9):196-209

WHAT INSIGHT CAN WE EXTRACT FROM THE METHOD? PSP  TP  CM  CASP  INS

Is all that information useful? ,[object Object],[object Object],[object Object]

Rule generated by BioHEL ,[object Object],[object Object]

Understanding the rule sets ,[object Object],[object Object],[object Object],[object Object]

Distribution of frequency of use of attributes ,[object Object],[object Object]

Top 10 attributes The four kind of residue’s predictions are highly ranked Attribute Frequency Counts PredSS_r1_1 1.48% 18141 PredCN_r1 1.66% 20336 propensity 1.74% 21288 PredSS_r2 1.75% 21350 PredSS_r1 1.82% 22205 PredRCH_r2 1.87% 22856 PredRCH_r1 2.04% 24961 PredSA_r2 2.12% 25891 PredSA_r1 2.39% 29246 separation 4.17% 50951

Beyond individual attributes… ,[object Object],[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

CM prediction. Is it worth it? ,[object Object],[object Object]

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Data Mining Protein Structures' Topological Properties to Enhance Contact Map Predictions

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Data Mining Protein Structures' Topological Properties to Enhance Contact Map Predictions