Exact structure match queries against BindingDB between September 2004 and August 2012

Exact structure match queries against BindingDB between September 2004 and August 2012

The queries were generated by users of the BindingDB web interface between September 2004 and mid-August of 2012. Structures were sketched using Marvin.

If you use this data set, please cite:

  Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK.
  BindingDB: a web-accessible database of experimentally determined
    protein-ligand binding affinities.
  Nucleic Acids Res. 2007 Jan;35(Database issue):D198-201.
  doi: 10.1093/nar/gkl999
  Epub 2006 Dec 1
  PMID: 17145705
  PMCID: PMC1751547
  https://doi.org/10.1093%2Fnar%2Fgkl999

The included files are:

README
------

A text file with more details about the data sets and their provenance.

exact.dat.zstd
--------------

The processed data set with 3,414,228 queries, one query per line. The file is compressed using Zstandard. The queries are a combination of CXSMILES, non-standard SMILES, and non-SMILES strings.

BindingDB_exact.dat
-------------------

A cleaned-up subset with 119,883 entries, one entry per line. Each entry has two columns, separated by a tab. The first column is the (possibly cleaned-up) CXSMILES from the source data, the second is the number of times the CXSMILES occurs in the source data. Each CXSMILES is present only once in the data set.

NOTE: the CXSMILES have not be canonicalized. Canonicalization using RDKit 2021.09.4 results in 94,362 unique queries, but causes the extended CXSMILES annotations to disappear.

bindingdb_cleanup.py
--------------------

The Python program used to convert exact.dat.zstd to BindingDB_exact.dat.

History
=======

15 August 2012
--------------

Contribution to the SQC.

Tiqing Lui

18 Aug 2012
-----------

Initial import into the SQC

Andrew Dalke

28 Aug 2022
-----------

Ported bindingdb_cleanup.py to Python 3.

Added cleanup methods to add brackets to "(O-)", "C@@", "nH", and "NH" when appropriate.

Simplified bindingdb_cleanup.py by dropping support for tools other than RKit.

Updated for distribution on Zenodo.

Andrew Dalke