1. Rosetta Energy Function Glenn Butterfoss

2. Rosetta Energy Function Major Classes: 1. Low resolution: Reduced atom representation Simple energy function Aggressively search conformational space 2. High resolution: Full atom More sophisticated energy function “Local” search of conformational (and sequence) space

3. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions)

4. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) In general … Weighted linear combination Energy = w 1 *term 1 + w 2 *term 2 + … Pair-wise decomposable Heavily trained on PDB statistics Discriminate “near native” vs “non native” No single low resolution score Several functions with different weights

5. Rosetta Energy Function 11 22 Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions)

6. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) d E CLASH BAD!! Evaluate between Centoids and Backbone Atoms

7. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) Pair-wise probability based on PDB statistics (electrostatics) aa = residue type d = centroid distance (binned, interpolated) s = sequence seperation (must be > 8 res )

8. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) neighbors within 10 Å of C  binned by : 0-3, 4,5, …, >30 also interpolated Probability of burial /exposure (solvation)

9. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) Optimize 2º orientation

10. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) N R1R1 R2R2 C O Represent protein as vectors of 2 residue “strands” sheet vector helix vector

11. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) Coordinate system v1v1 v2v2    r hb Scores selected to discriminate “near native structures for “non native”: Relative direction (  ) Relative H-bond orientation (hb) Distance (r, r  Number of sheets given number of strands Helix-Strand Packing

12. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) Used in earlier stages and for filtering Promote a compact fold

13. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) LTSDELKAQWNTSTLVRHQEAGASLTSDELKAQWNTSTLVRHQEAGAS set of non-redundant protein structures......

14. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions) NC + N C Fragment insertion Extended protein chain N C + Select a site Fragment insertion

15. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies In general … Weighted linear combination Energy = w 1 *term 1 + w 2 *term 2 + … Pair-wise decomposable Pre- tabulate energies Hybrid Statistical / MM-like score Weights trained for different applications

16. Rosetta Energy Function 11 22 High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies

17. experimental conformation rotamer Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies rotamers

18. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies 11 22 Dunbrack and Cohen library Based on PDB statistics Backbone dependent Additional rotamers from standard deviations of distributions

19. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies 11 22 ss = secondary structure Local backbone energy Also used in some centroid refinement

20. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies Fast pair-wise additive Penalize burial of polar residues Simple solvation model Lazaridius Karplus (standard)

21. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies Protein-DNA interactions: Generalized Born Protein-Ligand: Coulomb Simple solvation model (Special cases)

22. Rosetta Energy Function H O O High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies Geometric H-bond potential 2 angles, 1 distance Based on PDB statistics r H-bonding

23. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies r CHARMM radii Standard attractive potential Repulsive term linearized Note: command line options allow the repulsive term to be softened (radii reduced) VDW interactions

24. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies Probability of finding residue types at give in distance Defined by C  coordinates Electrostatics

25. Rosetta Energy Function High resolution: Atom Model full atom representation Energy function terms Rotamer (Dunbrack) Ramachandran Solvation (Lazaridius Karplus) Hydrogen bonding Lennard-Jones Pair (electrostatic) Reference energies Unique “cost” for designing in each residue type  G for bringing residue type into folded protein Optimized with sequence recovery trials of folded protein structures Correction for “folding”

26. Rosetta Energy Function Xavier Rosetta Community Thanks

27. Rosetta in Systems Biology Structure Prediction: Monte Carlo + Minimization search p(ΔE)? Energy

28. Rosetta in Systems Biology Protein Design: Protocol: Packing: Pre-tabulate table of all pair-wise rotamer energies Monte Carlo search through rotamer / sequence space With docking and backbone movement: Iterate packing with (as above) with backbone / rigid body movements Possibly apply restraints docking, rmsd, disulfide, …

29. Rosetta in Systems Biology Protein Design: Protocol: Filtering: Total energy Packing quality Avoid buried unsatisfied H-bonds (problem at interfaces)

30. Rosetta Energy Function Low resolution: Atom Model centroid reduction of side chains Energy function terms van der Waals repulsion “pair” terms (electrostatics) residue environment (prob of burial) 2º structure pairing terms (H-bonds) radius of gyration packing density Implicit terms fragments (local interactions)