Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

method for protein structure modeling5. Our loop reconstruction protocol iterates KIC calculations as Monte Carlo moves first with loop backbone minimization in a low-resolution stage, in which side-chains are represented as centroids, and then in a high-resolution all-atom stage with minimization of the loop backbone and all side chains in the loop environment (Supplementary Fig. 2 and Supplementary Methods). At the beginning of each KIC simulation, we discard all native loop bond lengths, bond angles and torsions. In addition, we perform reconstructions without knowledge of native side-chain conformations in both the loop and the protein scaffold (Supplementary Methods), which makes prediction substantially more challenging but broadens the range of applications to designing new loop conformations that may interact differently with neighboring side chains. We found that KIC substantially improves model accuracy over the standard loop building method in Rosetta, which combines insertion of torsion segments from homologous proteins and a numerical closure technique6. We generated 1,000 models by the KIC method and compared its performance to the standard Rosetta method with the same number of Monte Carlo steps on twentyfive 12-residue protein loops (dataset 1; ref. 7). For each protein, we computed the root mean squared (r.m.s.) deviation of the backbone atoms of the best scoring loop model to the crystallographic loop, after superimposing the non-loop regions of the model onto the crystal structure. The KIC protocol frequently sampled regions of conformational space that were <1.0 A from the crystallographic loop, which were not sampled by the standard Rosetta method (Fig. 1b). In the majority of cases (15/25), the best-scoring models were very close to the crystallographic loop conformation (Fig. 1b,c). in many species not yet considered genetically tractable. SHOREmap could also be applied to mapping of quantitative trait loci, large deletions and recessive lethal or dominant mutations (Supplementary Note).