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WONKA: objective novel complex analysis for ensembles of protein–ligand structures

A. R. Bradley, I. D. Wall, F. von Delft, D. V. S. Green, C. M. Deane, B. D. Marsden
2015 Journal of Computer-Aided Molecular Design  
WONKA is a tool for the systematic analysis of an ensemble of protein-ligand structures. It makes the identification of conserved and unusual features within such an ensemble straightforward.  ...  WONKA uses an intuitive workflow to process structural co-ordinates. Ligand and protein features are summarised and then presented within an interactive web application.  ...  Acknowledgments We would like to thank Paul Brennan and Oakley Cox for extensive help in driving the features available in WONKA and for useful discussion on the project.  ... 
doi:10.1007/s10822-015-9866-z pmid:26387008 pmcid:PMC4621702 fatcat:hhxx4umeyfgh5ag3lrfmuqjk5i

DNA-based construction at the nanoscale: emerging trends and applications

P Lourdu Xavier, Arun Richard Chandrasekaran
The field of structural DNA nanotechnology has evolved remarkably—from the creation of artificial immobile junctions to the recent DNA–protein hybrid nanoscale shapes—in a span of about 35 years.  ...  In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures.  ...  (A) DNA 7 nanotubes for aligning proteins for NMR analysis (top) [123] and structure of a mitochondrial uncoupling 8 protein solved using DNA nanotubes [125] (B) DNA junction based 2D arrays to host protein  ... 
doi:10.3204/pubdb-2018-00385 fatcat:kjttyvcqv5ht3ncseuaco25k5q