scholarly journals PDBcle – An online tool for extracting chain structure and sequence of macromolecule and small molecule structure from the Protein Data Bank

2021 ◽  
Vol 14 (16) ◽  
pp. 1296-1301
Author(s):  
T Ashok Kumar ◽  
Keyword(s):  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank ◽  
Chain Structure ◽  
Online Tool ◽  
Molecule Structure

On the propagation of errors

2013 ◽  
Vol 69 (10) ◽  
pp. 1865-1866 ◽  
Author(s):  
Mariusz Jaskolski
Keyword(s):  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank ◽  
Propagation Of Errors ◽  
Small Molecule Ligand

The policy of the Protein Data Bank (PDB) that the first deposition of a small-molecule ligand, even with erroneous atom numbering, sets a precedent over accepted nomenclature rules is disputed. Recommendations regarding ligand molecules in the PDB are suggested.

scholarly journals A complete small molecule dataset from the protein data bank

FEBS Letters ◽  
2006 ◽  
Vol 580 (6) ◽  
pp. 1649-1653 ◽  
Author(s):  
Howard J. Feldman ◽  
Kevin A. Snyder ◽  
Amy Ticoll ◽  
Greg Pintilie ◽  
Christopher W.V. Hogue
Keyword(s):  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank

scholarly journals Small-molecule ligand/drug representation and validation in the Protein Data Bank

2017 ◽  
Vol 73 (a2) ◽  
pp. C45-C45
Author(s):  
Genji Kurisu ◽  
Stephen K. Burley ◽  
John L. Markley ◽  
Haruki Nakamura ◽  
Sameer Velankar
Keyword(s):  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank ◽  
Small Molecule Ligand

scholarly journals Small molecule annotation for the Protein Data Bank

Database ◽  
2014 ◽  
Vol 2014 (0) ◽  
pp. bau116-bau116 ◽  
Author(s):  
S. Sen ◽  
J. Young ◽  
J. M. Berrisford ◽  
M. Chen ◽  
M. J. Conroy ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank

scholarly journals Simplified quality assessment for small-molecule ligands in the Protein Data Bank

Structure ◽  
2022 ◽  
Author(s):  
Chenghua Shao ◽  
John D. Westbrook ◽  
Changpeng Lu ◽  
Charmi Bhikadiya ◽  
Ezra Peisach ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank ◽  
Small Molecule Ligands
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