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1.  Completion of autobuilt protein models using a database of protein fragments 
Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules.
Two developments in the process of automated protein model building in the Buccaneer software are presented. A general-purpose library for protein fragments of arbitrary size is described, with a highly optimized search method allowing the use of a larger database than in previous work. The problem of assembling an autobuilt model into complete chains is discussed. This involves the assembly of disconnected chain fragments into complete molecules and the use of the database of protein fragments in improving the model completeness. Assembly of fragments into molecules is a standard step in existing model-building software, but the methods have not received detailed discussion in the literature.
doi:10.1107/S0907444911039655
PMCID: PMC3322592  PMID: 22505253
model building; databases; Buccaneer
2.  From crystal to structure with CCP4 
An introduction to the proceedings of the CCP4 study weekend is given.
doi:10.1107/S0907444911007578
PMCID: PMC3069737  PMID: 21460440
CCP4
3.  Recent developments in classical density modification 
Several new methods are evaluated for use in the improvement of experimental phases in the framework of a classical density-modification calculation. These methods have been implemented in a new computer program, Parrot.
Classical density-modification techniques (as opposed to statistical approaches) offer a computationally cheap method for improving phase estimates in order to provide a good electron-density map for model building. The rise of statistical methods has lead to a shift in focus away from the classical approaches; as a result, some recent developments have not made their way into classical density-modification software. This paper describes the application of some recent tech­niques, including most importantly the use of prior phase information in the likelihood estimation of phase errors within a classical density-modification framework. The resulting software gives significantly better results than comparable classical methods, while remaining nearly two orders of magnitude faster than statistical methods.
doi:10.1107/S090744490903947X
PMCID: PMC2852311  PMID: 20383000
density modification; phase improvement; Parrot
4.  Fitting molecular fragments into electron density 
A number of techniques for the location of small and medium-sized model fragments in experimentally phased electron-density maps are explored. The application of one of these techniques to automated model building is discussed.
Molecular replacement is a powerful tool for the location of large models using structure-factor magnitudes alone. When phase information is available, it becomes possible to locate smaller fragments of the structure ranging in size from a few atoms to a single domain. The calculation is demanding, requiring a six-dimensional rotation and translation search. A number of approaches have been developed to this problem and a selection of these are reviewed in this paper. The application of one of these techniques to the problem of automated model building is explored in more detail, with particular reference to the problem of sequencing a protein main-chain trace.
doi:10.1107/S0907444907033938
PMCID: PMC2394793  PMID: 18094471
model fragments; electron-density maps; model building

Results 1-4 (4)