Facilitating Molecular Biology Teaching by Using Augmented Reality (AR) and Protein Data Bank (PDB)

TechTrends ◽  
2018 ◽  
Vol 63 (2) ◽  
pp. 188-193 ◽  
Author(s):  
Parviz Safadel ◽  
David White
2009 ◽  
Vol 42 (6) ◽  
pp. 1035-1042 ◽  
Author(s):  
Fabrice Gorrec

A 96-condition initial screen for protein crystallization, called MORPHEUS, has been developed at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). The concept integrates several innovative approaches, such as chemically compatible mixes of potential ligands, new buffer systems and precipitant mixes that also act as cryoprotectants. Instead of gathering a set of crystallization conditions that have already been successful, a selection of molecules frequently observed in the Protein Data Bank (PDB) to co-crystallize with proteins has been made. These have been put together in mixes of similar chemical behaviour and structure, and combined with buffers and precipitant mixes that were also derived from PDB searches, to build the screende novo. Observations made at the MRC-LMB and many practical aspects were also taken into account when formulating the screen. The resulting screen is easy to use, comprehensive yet small, and has already yielded a list of crystallization hits using both known and novel samples. As an indicator of success, the screen has now become one of the standard screens used routinely at the MRC-LMB when searching initial crystallization conditions for biological macromolecules.


2002 ◽  
Vol 58 (s1) ◽  
pp. c214-c214
Author(s):  
W. F. Bluhm ◽  
T. Battistuz ◽  
E. Clingman ◽  
N. Deshpande ◽  
W. Fleri ◽  
...  

2021 ◽  
pp. 166900
Author(s):  
Alexander Miguel Monzon ◽  
Paolo Bonato ◽  
Marco Necci ◽  
Silvio C.E. Tosatto ◽  
Damiano Piovesan
Keyword(s):  

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn–Cys distances and Cys–Zn–Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.


2018 ◽  
Vol 47 (D1) ◽  
pp. D520-D528 ◽  
Author(s):  
◽  
Stephen K Burley ◽  
Helen M Berman ◽  
Charmi Bhikadiya ◽  
Chunxiao Bi ◽  
...  

2017 ◽  
Vol 27 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Akira R. Kinjo ◽  
Gert-Jan Bekker ◽  
Hiroshi Wako ◽  
Shigeru Endo ◽  
Yuko Tsuchiya ◽  
...  
Keyword(s):  

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