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Example for SCP-problem PDB code: 2OL9 #Resides : 6 ① SER ② ASN ④ ASN ⑤ ASN ⑥ PHE ③ GLN 1 ① SER ② ASN ④ ASN ⑤ ASN ⑥ PHE ③ GLN.

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Presentation on theme: "Example for SCP-problem PDB code: 2OL9 #Resides : 6 ① SER ② ASN ④ ASN ⑤ ASN ⑥ PHE ③ GLN 1 ① SER ② ASN ④ ASN ⑤ ASN ⑥ PHE ③ GLN."— Presentation transcript:

1 Example for SCP-problem PDB code: 2OL9 #Resides : 6 ① SER ② ASN ④ ASN ⑤ ASN ⑥ PHE ③ GLN 1 ① SER ② ASN ④ ASN ⑤ ASN ⑥ PHE ③ GLN

2 Size of Solution Space 2

3 Mixed Integer Linear Programming (MILP) Formulation 3 Kingsford et al. (Structural Bioinformatics, 05) Eriksson et al. (LNCS, 01) Zhu (Ind. Eng. Chem. Res., 07)

4 Tyrosine Threonine SCP-problem: 2-body Formulation –Between backbone and side-chain –Between two side-chains Applies to all pairwise atoms Ignores tripletwise (or higher) atomic interactions  Still NP-hard 4

5 Between two atoms : C and O van der Waals Force 5 ( Lenard-Jones Potential ) J.E. Lennard-Jones. Cohesion. In Proceedings of the Physical Society, vol. 43, pp.461-482, 1931.

6 LJ-potential vs. Intersection Volume 6

7 ① ② ③ ④ ⑤ ⑥ 7 BetaSCP2: Intersection Volume Minimization

8 References BetaSCP1 BetaSCP2 8

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