• Automating tasks in protein st...

Treffer: Automating tasks in protein structure determination with the clipper python module.

Title:
Automating tasks in protein structure determination with the clipper python module.
Authors:
McNicholas S; Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom., Croll T; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom., Burnley T; STFC Rutherford Appleton Laboratory OX11 0QX, Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM), United Kingdom., Palmer CM; STFC Rutherford Appleton Laboratory OX11 0QX, Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM), United Kingdom., Hoh SW; Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom., Jenkins HT; Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom., Dodson E; Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom., Cowtan K; Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom., Agirre J; Department of Chemistry, York Structural Biology Laboratory, The University of York, York, YO10 5DD, United Kingdom.
Source:
Protein science : a publication of the Protein Society [Protein Sci] 2018 Jan; Vol. 27 (1), pp. 207-216. Date of Electronic Publication: 2017 Nov 06.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE
Imprint Name(s):
Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press
Original Publication: New York, N.Y. : Cambridge University Press, c1992-
MeSH Terms:
Databases, Protein* , Programming Languages*, Proteins/*chemistry, Cryoelectron Microscopy ; Protein Conformation
References:
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Grant Information:
BB/P000517/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/P000975/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; MR/N009614/1 United Kingdom MRC_ Medical Research Council; BB/L006383/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; United Kingdom WT_ Wellcome Trust; MR/N009614/1 United Kingdom MRC_ Medical Research Council; MR/J000825/1 United Kingdom MRC_ Medical Research Council
Contributed Indexing:
Keywords: Clipper; NumPy; Python; SWIG; automation; crystallography; electron cryo-microscopy; libraries; pipelines; scripting
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20170914 Date Completed: 20171226 Latest Revision: 20250825
Update Code:
20250826
PubMed Central ID:
PMC5734304
DOI:
10.1002/pro.3299
PMID:
28901669
Database:
MEDLINE

Weitere Informationen

Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module.
(© 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.)