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pywindow: automated structural analysis of molecular pores

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Title: pywindow: automated structural analysis of molecular pores
Authors: Miklitz, M
Jelfs, K
Item Type: Journal Article
Abstract: Structural analysis of molecular pores can yield important information on their behavior in solution and in the solid state. We developed pywindow, a python package that enables the automated analysis of structural features of porous molecular materials, such as molecular cages. Our analysis includes the cavity diameter, number of windows, window diameters, and average molecular diameter. Molecular dynamics trajectories of molecular pores can also be analyzed to explore the influence of flexibility. We present the methodology, validation, and application of pywindow for the analysis of molecular pores, metal–organic polyhedra, and some instances of framework materials. pywindow is freely available from github.com/JelfsMaterialsGroup/pywindow.
Issue Date: 24-Dec-2018
Date of Acceptance: 1-Sep-2018
URI: http://hdl.handle.net/10044/1/63083
DOI: https://dx.doi.org/10.1021/acs.jcim.8b00490
ISSN: 1549-9596
Publisher: American Chemical Society
Start Page: 2387
End Page: 2391
Journal / Book Title: Journal of Chemical Information and Modeling
Volume: 58
Issue: 12
Copyright Statement: © 2018 American Chemical Society. This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Sponsor/Funder: The Royal Society
Engineering & Physical Science Research Council (EPSRC)
Engineering & Physical Science Research Council (EPSRC)
Commission of the European Communities
Funder's Grant Number: UF120469
EP/M017257/1
EP/P005543/1
758370
Keywords: Science & Technology
Life Sciences & Biomedicine
Physical Sciences
Technology
Chemistry, Medicinal
Chemistry, Multidisciplinary
Computer Science, Information Systems
Computer Science, Interdisciplinary Applications
Pharmacology & Pharmacy
Chemistry
Computer Science
ORGANIC CAGES
FORCE-FIELD
SIMULATIONS
LANDSCAPES
DYNAMICS
DESIGN
TOOLS
0304 Medicinal And Biomolecular Chemistry
0307 Theoretical And Computational Chemistry
0802 Computation Theory And Mathematics
Medicinal & Biomolecular Chemistry
Publication Status: Published
Online Publication Date: 2018-09-10
Appears in Collections:Chemistry
Faculty of Natural Sciences