Prediction of the Number of Residue Contacts in Proteins

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Presentation transcript:

Prediction of the Number of Residue Contacts in Proteins 발표자: 정 제 균 Fiero Fariselli and Rita Casadio CIRB Biocomputing Unit and Lab. of Biophysics, Dept. Biology University of Bologna

Introduction The elucidation of the functional properties of protein The process of protein folding Three-dimensional structure Residue contacts constrain protein folding and characterize different protein structure. Knowing the correct positions of residue contacts in protein has been proven extremely useful to determine the three-dimensional structure.

2D Protein Prediction: An Overview

Binary Version: Prediction of Contacts

Computation of Residue Solvent Accessibility and Contact Number using the DSSP program (Kabsch and Sander 1983) The value is normalized to the maximal exposed surface area of each residue (Rose et al., 1985). The number of inter-residue contacts for each residue defining a spherical protein volume centered in the C atom (or C for GLY) and with a radius to 6.5

The Predicator Back-propagation one hidden layer two output neurons The number of hidden neuron – from 2 to 32 The input window – 1 to 15 residue long A cross validation procedure

Neural Networks Input Coding

Frequency Distribution of the Relative Solvent Accessibility

Frequency Distribution of the Number of Contacts