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TEMPy specifications

Information


Unique identifier OMICS_26708
Name TEMPy
Alternative name Template and EM comparison using PYthon
Software type Framework/Library, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A density map or an atomic structure.
Input format CCP4/MPC,PDB,mmCIF
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
matplotlib, numpy, scipy, biopython
Maintained Yes

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  • person_outline Maya Topf <>

Publication for Template and EM comparison using PYthon

TEMPy in publications

 (10)
PMCID: 5767682
PMID: 29196491
DOI: 10.1124/mol.117.110551

[…] improve the fit of the loop between tm1 and tm2, loop modeling was carried out with modeller, generating 200 loops. the loops were ranked by their segment-based cross-correlation coefficient using tempy (), with the highest-ranking loop (with a segment-based cross-correlation coefficient of 0.82) clearly following the density shape. in the third stage, the model containing the refined loop […]

PMCID: 5692573
PMID: 29078367
DOI: 10.1073/pnas.1712169114

[…] that the kinetically atp-competitive inhibition of kif18a by btb-1 occurs through an allosteric structural mechanism., to further understand the mechanism of kif18a inhibition by btb-1 (), we used tempy () to calculate the difference map between the btb-1–bound and the nn kif18a_mdnl cryo-em reconstructions (, orange density). as expected, some regions of difference density corresponded […]

PMCID: 5544394
PMID: 28798962
DOI: 10.1126/sciadv.1701726

[…] () was then used for refinement of secondary structures and loops in the map. energy minimization to fix geometry was performed in phenix (). quality and improvement of the fit were assessed with tempy () using the segment-based manders’ overlap coefficient scores and segment-based cross-correlation scores (). quality of the fit in different regions is highlighted in fig. s8. for the ground […]

PMCID: 5479444
PMID: 28552721
DOI: 10.1016/j.jsb.2017.05.007

[…] on the ‘extent of surface exposure’. we show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features. all the scores discussed are implemented in tempy (http://tempy.ismb.lon.ac.uk/)., a major leap in structure characterization of large bio-molecular machines and cellular components has been brought in by biophysical techniques like electron […]

PMCID: 5414403
PMID: 28512576
DOI: 10.1107/S2052252517005115

[…] that are compatible with the placement of the second subunit in such a way as to satisfy the predicted contacts. thirdly, programs for the automated fitting of structures to density such as gamma-tempy (pandurangan et al., 2015) or 3diana (segura et al., 2016) could be engineered to directly include satisfaction of predicted contact information in their scoring functions. more speculatively, […]


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TEMPy institution(s)
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK; Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
TEMPy funding source(s)
Supported by BBSRC (BB/ K01692X/1), MRC (G0600084), Leverhulme Trust (RPG-2012-519) and the European Commission within the Research Infrastructures of the FP7 Capacities Specific Programme (contract Biomedbridges No. 284209).

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