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Some functions

Some functions. Introduction- Amino Acid. Cd.  2. Cg. Cb.  1. Ca. N. phi= R i-1 .c, R i .n, R i .ca, R i .c psi= R i .n, R i .ca, R i+1 .c, R i+1 .n. Angle. Given three points  angle Inner product. Cross Product. Cross product. Dihedral angle.

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Some functions

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  1. Some functions

  2. Introduction- Amino Acid Cd 2 Cg Cb 1 Ca N phi= Ri-1.c, Ri.n, Ri.ca, Ri.c psi= Ri.n, Ri.ca, Ri+1.c,Ri+1 .n

  3. Angle • Given three points  angle • Inner product

  4. Cross Product • Cross product

  5. Dihedral angle • Given 4 point (a, b, c, d)  dihedral angle • a, b, c: have a plane (p1) • b, c, d: have another plane (p2) • Normal vectors to p1 and p2: v1 and v2 • (v1, original point, v2): decide an angle

  6. Protein Structure: HIV-1 (A-chain) (1hvr ) Backbone with residue number Backbone with side chain Backbone

  7. Side Chain Prediction - Problem Cd 2 Cg Cb 1 Ca N Backbone with side chain • Given main chain, determining the side-chain conformation • dihedral angles of residues • positions of atoms • Search space • 100 : 36 of each dihedral angles • N36: R is the number of dihedral angles (N:40-1000) • Side-chain optimization • Determining initial assignment rules • Determining best conformation of side-chain • Collision avoiding • Objective function (energy function) • energy minimization procedure

  8. Side Chain Prediction - Rotamer Cd 2 Cg Cb 1 PDB (814 chains) Ca N build the distribution of each dihedral angle of Amino acid (18) (NN, statistics) • Rotamer Library • Backbone independent relation (87) • Backbone dependent relation (93) • Environment relation

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