Prediction of Protein Binding Sites in Protein Structures Using Hidden Markov Support Vector...
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Prediction of Protein Binding Sites in Protein Structures Using Hidden Markov Support Vector Machine
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Slate: the target protein.Blue: the binding partner.Magenta: interface residues.
SSSEIKIVRDEYGMPHIYANDTWHLFYGYG
IIINIINNIINNNIIIIIIINIINIIINNN
Input
Output
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Machine Learning Methods Applied
Classification methods
Sequential labelling methods
ANN
SVM
CRF
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FEATURES
• Neighboring residue profile feature• Hydrophobicity• Sequence conservation• Secondary structure• Solvent accessible surface area
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Hidden Markov Support Vector Machine
Discriminant function
Emission feature function
Transition feature function
Corresponding weight
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Hidden Markov Support Vector Machine
Spatially neighboring residue profile feature
𝑒𝑦 ,𝑎𝑎𝑝𝑟𝑜𝑓𝑖𝑙𝑒 (𝑥𝑘 , 𝑦 𝑖 )={L (𝑃𝑆𝑆𝑀 (𝑥𝑘 ,𝑎𝑎 )) ,∧if 𝑦 𝑖=𝑦
0 ,∧otherwise
Spatially neighboring residue accessible surface (ASA) feature
𝑒𝑦𝐴𝑆𝐴 (𝑥𝑘 , 𝑦 𝑖 )={ASA (𝑥𝑘) ,∧if 𝑦 𝑖=𝑦
0 ,∧otherwise
Emission feature function
𝐿 (𝑥 ){ 0 𝑖𝑓 𝑥≤−512+ 𝑥10
𝑖𝑓 −5<𝑥<5
1 h𝑜𝑡 𝑒𝑟𝑤𝑖𝑠𝑒
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Hidden Markov Support Vector Machine
Discriminant function
Transition feature function
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Hidden Markov Support Vector Machine
Transition feature function
𝑡𝑦 ,𝑦 ′ (𝑥 , 𝑦 𝑖− 1 , 𝑦 𝑖 )={1 ,∧if 𝑦 𝑖−1= y∧𝑦 𝑖=𝑦0 ,∧otherwise
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Hidden Markov Support Vector Machine
Discriminant functionCorresponding weight
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Hidden Markov Support Vector Machine
Optimization problem
s.t.
Source Code: http://www.cs.cornell.edu/People/tj/svm_light/svm_hmm.html
☆ The cutting-plane algorithm makes it linear
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DATA SET
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𝐅𝟏=𝟐×𝑺𝒑𝒆𝒄𝒊𝒇𝒊𝒄𝒊𝒕𝒚+¿×
𝑺𝒆𝒏𝒔𝒊𝒕𝒊𝒗𝒊𝒕𝒚+¿
𝑺𝒑𝒆𝒄𝒊𝒇𝒊𝒄𝒊𝒕𝒚 +¿+𝑺𝒆𝒏𝒔𝒊𝒕𝒊𝒗𝒊𝒕𝒚 +¿ ¿¿¿¿
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𝐀𝐜𝐜𝐮𝐫𝐚𝐜𝐲=𝑻𝑷 +𝑻𝑵
𝐓𝐏+𝑻𝑵+𝑭𝑷+𝑭𝑵
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𝐌𝐂𝐂=𝑻𝑷×𝑻𝑵 −𝑭𝑷×𝑭𝑵
√ (𝐓𝐏+𝐅𝐍 ) (𝑻𝑷+𝑭𝑷 ) (𝑻𝑵+𝑭𝑷 ) (𝑻𝑵+𝑭𝑵 )
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Influence of the number of training samples on the prediction performance and running time
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Influence of the number of training samples on the prediction performance and running time
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The inter-relation information between neighboring residues is relevant for discrimination
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The window size has not significant influence on the performance
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Actual interface residues ANN
SVM CRF HM-SVM
Comparison with related methods
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Actual interface residues ANN
SVM CRF HM-SVM
Comparison with related methods
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SUMMARY
• Prediction of protein binding sites• Hidden Markov Support Vector Machine• Result Analysis
• Comparison with other methods• Influence of the number of training samples• The information between neighboring residues• Window size
• Discussion
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