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Acta Crystallographica Section D: Biological Crystallography (1)
Acta Crystallographica Section F: Structural Biology and Crystallization Communications (1)
Fazio, Vincent J. (2)
Bolton, Evan E. (1)
Gallagher, D. Travis (1)
Keegan, Ronan M. (1)
Long, Fei (1)
Lovell, David (1)
Luft, Joseph R. (1)
Murshudov, Garib N. (1)
Müller-Dieckmann, Jochen (1)
Newman, Janet (1)
Peat, Thomas S. (1)
Ratcliffe, David (1)
Sayle, Roger A. (1)
Snell, Edward H. (1)
Taylor, Kerry (1)
Vagin, Alexei A. (1)
Vallotton, Pascal (1)
Velanker, Sameer (1)
Winn, Martyn D. (1)
von Delft, Frank (1)
Year of Publication
On the need for an international effort to capture, share and use crystallization screening data
Bolton, Evan E.
Gallagher, D. Travis
Luft, Joseph R.
Peat, Thomas S.
Sayle, Roger A.
Snell, Edward H.
von Delft, Frank
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
Development of an ontology for the description of crystallization experiments and results is proposed.
When crystallization screening is conducted many outcomes are observed but typically the only trial recorded in the literature is the condition that yielded the crystal(s) used for subsequent diffraction studies. The initial hit that was optimized and the results of all the other trials are lost. These missing results contain information that would be useful for an improved general understanding of crystallization. This paper provides a report of a crystallization data exchange (XDX) workshop organized by several international large-scale crystallization screening laboratories to discuss how this information may be captured and utilized. A group that administers a significant fraction of the world’s crystallization screening results was convened, together with chemical and structural data informaticians and computational scientists who specialize in creating and analysing large disparate data sets. The development of a crystallization ontology for the crystallization community was proposed. This paper (by the attendees of the workshop) provides the thoughts and rationale leading to this conclusion. This is brought to the attention of the wider audience of crystallographers so that they are aware of these early efforts and can contribute to the process going forward.
crystallization screening data; crystallization ontology
Evaluating the solution from MrBUMP and BALBES
Keegan, Ronan M.
Winn, Martyn D.
Murshudov, Garib N.
Vagin, Alexei A.
Acta Crystallographica Section D: Biological Crystallography
The automated pipelines for molecular replacement MrBUMP and BALBES are reviewed, with an emphasis on understanding their output. Conclusions are drawn from their performance in extensive trials.
Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large-scale testing of the software.
MrBUMP; BALBES; molecular replacement
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