Automated Molecular Replacement Part 1: Automating Amore Make Amore as easy to use as Molrep, Phaser. Part 2: Construction of “best” model for Phaser Enable maximum number of structures to be solved using MR.

Amore Solution Process 1. Estimate number of molecules in Asymmetric unit (MATTHEWS). 2. Solve for first molecule (AUTO-AMORE) a) Rotation function. Euler angles { (α,β,γ) } b) Translation function. Euler angles + fractional translations { (x,y,z)} c) Fitting = Rigid Body Refinement 3. Solve for additional molecules. Extra translations. (iterative) 4. Final round of fitting 5. Apply rotations and translations to atom coordinates. (PDBSET ) 6. Merge into one pdb file. 7. Check for clashing (DISTANG)

Solution for n molecules Take top 5 (distinct) translation solutions from n – 1 molecule solution Take top 5 (distinct) rotation solutions Consider all possible combinations Search for translation solutions for 1 more molecule Score by summing correlation coefficients over all n molecules Sort solutions in order of decreasing score

Test Results Target Model % seq no. mols Solved 1n5b 1k6z 97 4 Yes 1nio 1ggp_A 1 1cv7 1gfl 96 1k6d 1o91 2 1mzr 1a80 51 1h5q 1v18a 34 12 No

Future developments Incorporation in Ronan’s pipeline Model Building using Arp/Warp

PART 2 Construction of “best model” for phaser Apply sequence alignment algorithm PSIBLAST : sequence – profile alignment FFAS : profile – profile alignment Modify template (Chainsaw) If Target R = Template R retain If not … R. Schwarzenbacher et al, Acta Cryst D60 1229, (2004)

Chainsaw Template Target Action >= Serine Prune to CG Alanine Prune to CB Glycine Prune to CA >= Alanine Add CB

Future work Use more sophisticated sequence alignment algorithms Apply to ensembles