Supplementary Material for the Paper: Threading Without Optimizing Weighting Factor for the Scoring Function
Proteins, in revision (2008)

Yifeng David Yang1, Daisuke Kihara1,2,3,4
1 Department of Biological Sciences, College of Science
2 Department of Computer Science, College of Science
3 Markey Center for Structural Biology
4 The Bindley Bioscience Center

Purdue University, West Lafayette, IN, 47907, USA

1. Angle Potential

Here is the Angle Potential that we use in the paper.This file contains 40 lines. The odd number line indicates the amino acid type, the even number line stores the angle potentials for the corresponding amino acid type.Angle potentials are sampled from a 36*36*36 grid on the tau,theta,tau dimention. An angle triad (tau1,theta1,tau2) corresponds to kth number of the line with the relationship k=36*36*int(theta1/5)+36*int(tau2/10)+int(tau1/10);

2. Contact Potential

Here is the Contact Potential used in the paper. There are 210 lines in the file, each line stores the potential for the specific amino acid pair.

Contact Information:
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Department of Biological Sciences
Purdue University
West Lafayette , IN, 47906
Tel: 765-494-2744
Email: dkihara@purdue.edu
yang41@purdue.edu