scholarly journals PDB-ML, an XML for Protein Data Bank, and a search system with it

2003 ◽  
Vol 43 (supplement) ◽  
pp. S112
Author(s):  
N. Ito ◽  
K. Kobayashi ◽  
H. Sakamoto ◽  
H. Nakamura
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Search System

scholarly journals The Protein Data Bank: data distribution and query functionality

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

FLIPPER: predicting and characterizing linear interacting peptides in the Protein Data Bank

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

scholarly journals Validation and correction of Zn–Cys x His y complexes

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Model Validation ◽  
Data Bank ◽  
Zinc Complexes ◽  
Zinc Ions ◽  
Tetrahedral Complex ◽  
Context Sensitive

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.

scholarly journals Protein Data Bank: the single global archive for 3D macromolecular structure data

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

scholarly journals New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

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