Supplementary Materials For the Paper:

Y. H. Tan, H. Huang, and D. Kihara
Proteins: Structure, Function and Bioinformatics 64: 587-600. (2006) See Publication page)

Lindahl and Elofsson's Dataset:

• Arne Elofsson's website
• seq.tar.gz Sequence dataset in FASTA format
• pdb.tar.gz Sequence dataset in PDB format

Matrices:

1. BLAJ Matrix built from structural superposition data for identifying potential remote homologues (Blake-Cohen, 2001)
2. BLOSUM45 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
3. JOHM Structure-based amino acid scoring table (Johnson-Overington, 1993)
4. KOLA Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
5. KOSJ Context-dependent optimal substitution matrices for all residues (Koshi-Goldstein, 1995)
6. MIYS Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
7. OVEJ STR matrix from structure-based alignments (Overington et al., 1992)
8. PRLA1 Structure derived matrix (SDM) for alignment of distantly related sequences (Prlic et al., 2000)
9. PRLA2 Homologous structure dereived matrix (HSDM) for alignment of distantly related sequences (Prlic et al., 2000)
10. QUC1 Cross-correlation coefficients of preference factors main chain (Qu et al., 1993)
11. QUC2 Cross-correlation coefficients of preference factors side chain (Qu et al., 1993)
12. QUIB STROMA score matrix for the alignment of known distant homologs (Qian-Goldstein, 2002)


13. CCPC
14. CCPG
15. CCPQ
16. CCREFPG
17. CC6PC
18. CC6PG
19. CC6PQ


20. CC10 10% CCPC + 90% KOLA
21. CC20 20% CCPC + 80% KOLA
22. CC30 30% CCPC + 70% KOLA
23. CC40 40% CCPC + 60% KOLA
24. CC50 50% CCPC + 50% KOLA
25. CC60 60% CCPC + 40% KOLA
26. CC70 70% CCPC + 30% KOLA
27. CC80 80% CCPC + 20% KOLA
28. CC90 90% CCPC + 10% KOLA


29. Fam01 Downhill simplex optimization of matrix CCPC using family level data
30. SFam01 Downhill simplex optimization of matrix CCPC using super family level data
31. Fold01 Downhill simplex optimization of matrix CCPC using fold level data
32. RANDMATRIX Matrix containing random values between -5 and 15

Golden Alignments:

• ce.fam.tar.gz Family level alignments computed using CE
• ce.sfam.tar.gz Super family level alignments computed using CE
• ce.fold.tar.gz Fold level alignments computed using CE

Benchmarking Datasets:

• BAliBASE 1.0
• Prefab 4.0
• Homstrad

Contact Information: