title: Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement.
abstract: AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England.
authors.forename: Jaclyn
authors.initials: J
authors.lastname: Bibby
authors.forename: Ronan M
authors.initials: RM
authors.lastname: Keegan
authors.forename: Olga
authors.initials: O
authors.lastname: Mayans
authors.forename: Martyn D
authors.initials: MD
authors.lastname: Winn
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Rigden
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D018360:Crystallography, X-Ray / Q000379:methods; D005544:Forecasting; D008958:Models, Molecular; D005810:Multigene Family; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017510:Protein Folding; D012984:Software / Q000592:standards; D048372:Streptomyces coelicolor / Q000737:chemistry / Q000235:genetics; D013879:Thioredoxins / Q000737:chemistry* / Q000235:genetics
chemical_list: D001425:Bacterial Outer Membrane Proteins; D013879:Thioredoxins
keywords: AMPLE; NMR structures; molecular replacement; search models