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Detection, delineation, measurement and display of cavities in macromolecular structures.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
1994 (English)In: Acta Crystallogr D Biol Crystallogr, ISSN 0907-4449, Vol. 50, no Pt 2, 178-85 p.Article in journal (Refereed) Published
Abstract [en]

A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program O. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using O. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.

Place, publisher, year, edition, pages
1994. Vol. 50, no Pt 2, 178-85 p.
Identifiers
URN: urn:nbn:se:uu:diva-21226PubMedID: 15299456OAI: oai:DiVA.org:uu-21226DiVA: diva2:48999
Available from: 2006-12-15 Created: 2006-12-15 Last updated: 2011-01-16

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