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

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 The Druggable Genome as Seen from the Protein Data Bank

2020 ◽  
Author(s):  
Jiayan Wang ◽  
Setayesh Yazdani ◽  
Ana Han ◽  
Matthieu Schapira
Keyword(s):  
Human Genome ◽  
Small Molecule ◽  
Data Bank ◽  
Specific Protein ◽  
Genome Project ◽  
Protein Families ◽  
Small Molecule Ligands ◽  
Human Proteins ◽  
Small Molecule Modulators ◽  
Druggable Genome

AbstractAlmost twenty years after the human genome was sequenced, the wealth of data produced by the international human genome project has not translated into a significantly improved drug discovery enterprise. This is in part because small molecule modulators that could be used to explore the cellular function of their target proteins and to discover new therapeutic opportunities are only available for a limited portion of the human proteome. International efforts are underway to develop such chemical tools for a few, specific protein families, and a “Target 2035” call to enable, expand and federate these efforts towards a comprehensive chemical coverage of the druggable genome was recently announced. But what is the druggable genome? Here, we systematically review structures of human proteins bound to drug-like ligands available from the protein databank (PDB) and use ligand desolvation upon binding as a druggability metric to draw a landscape of the human druggable genome. We show that the vast majority of druggable protein families, including some highly populated and deeply associated with cancer according to genomic screens, are almost orphan of small molecule ligands, and propose a list of 46 druggable domains representing 3440 human proteins that could be the focus of large chemical probe discovery efforts.

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
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