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Background. All-atom crystallographic refinement of proteins is a laboriousmanually driven procedure, as a result of which, alternative and multiconformerinterpretations are not routinely investigated.  Results. We describe efficient loop sampling procedures in Rappertk anddemonstrate that single loops in proteins can be automatically and accuratelymodelled with few positional restraints. Loops constructed with a compositeCNS/Rappertk protocol consistently have better Rfree than those with CNS alone.This approach is extended to a more realistic scenario where there are oftenlarge positional uncertainties in loops along with small imperfections in thesecondary structural framework. Both ensemble and collection methods are usedto estimate the structural heterogeneity of loop regions.  Conclusion. Apart from benchmarking Rappertk for the all-atom proteinrefinement task, this work also demonstrates its utility in both aspects ofloop modelling - building a single conformer and estimating structuralheterogeneity the loops can exhibit.

Crystallographic modelling of protein loops and their heterogeneity with Rappertk