libraries.md

@@ -2,38 +2,45 @@
 
 The following is a list of chemical libraries that we like to use in virtual screening exercises. This is only a small selection. The best way to browse compound collections is via [ZINC Subsets](http://zinc15.docking.org/substances/subsets/) and, especially, [ZINC Catalogs](http://zinc15.docking.org/catalogs/table.html). ZINC assigns an `abbreviation` to each collection, and we stick with ZINC notation if possible.
 
-* In the SB&NB file-system, compound collections can be found in `/aloy/web_checker/libraries/`.
-* The `chemical_checker` [PostGreSQL database](database) contains the compound collections, too, in the `libraries` table.
+In the SB&NB file-system, compound collections can be found in `/aloy/chemical_checker_repo/libraries/`. The `chemical_checker` [PostGreSQL database](database) contains the compound collections, too, in the `libraries` table.
 
-## Exemplar collections
+* [X] Included in the CC
+* [ ] Not yet included in the CC
 
-These are popular and representative compound libraries that we offer as default search libraries in the [Chemical Checker similarity resource](http://www.chemicalchecker.org).
-
-* Approved Drugs: `dbap` [[molecules](http://zinc15.docking.org/catalogs/dbap/)]. Approved drugs according to [DrugBank](https://www.drugbank.ca/).
-* Experimental Drugs `exd` [[molecules]()]. Experimental drugs according to [DrugBank](https://www.drugbank.ca/).
-* Human Metabolites `hmbdb`: [http://www.hmdb.ca/](http://www.hmdb.ca/). Human metabolites available from the Human Metabolome Database.
-* Traditional Chinese Medicines `tcm`: [http://tcm.cmu.edu.tw/](http://tcm.cmu.edu.tw/). Traditional Chinese Medicines from TCM@Taiwan database. This is the world's largest collection of Chinese medicines.
-* LINCS Compounds `lincs`: [http://lincsportal.ccs.miami.edu/SmallMolecules/](http://lincsportal.ccs.miami.edu/SmallMolecules/). Compounds, mainly from the Broad Institute Library, related to the LINCS consortium.
-* Prestwick Chemical Library `prestw`: [http://www.prestwickchemical.com/libraries-screening-lib-pcl.html](http://www.prestwickchemical.com/libraries-screening-lib-pcl.html). A commercial collection of over 1.2k off-patent drugs.
-* NIH Clinical Collection `nihcc`: []()
-* NCI Diversity Collection `ncidiv`: []()
-* Tool Compounds `tool`: []()
+## Exemplary collections
 
-## Screening libraries
+These are popular and representative compound libraries that we offer as default search libraries in the [Chemical Checker similarity resource](http://www.chemicalchecker.org).
 
-There is a large number number of chemogenomics databases that one may consider. I list here the ones selected in an important recent review on the matter: .
+* [X] Approved Drugs `dbap`: Approved drugs according to [DrugBank](https://www.drugbank.ca/) [[data](http://zinc15.docking.org/catalogs/dbap/)]
+* [X] Experimental Drugs `dbex`: Experimental drugs according to [DrugBank](https://www.drugbank.ca/) [[data](http://zinc15.docking.org/catalogs/dbex/)]
+* [X] Human Metabolites `hmbdb`: Human metabolites available from the [Human Metabolome Database](http://www.hmdb.ca/) [[data](http://zinc15.docking.org/catalogs/hmdb/)]
+* [X] Traditional Chinese Medicines `tcmnp`: Traditional Chinese Medicines from [TCM Database @ Taiwan](http://tcm.cmu.edu.tw/). This is the world's largest collection of Chinese medicines [[data](http://zinc15.docking.org/catalogs/tcmnp/)]
+* [X] LINCS Compounds `lincs`: Compounds, mainly from the Broad Institute Library, related to the [LINCS consortium]((http://lincsportal.ccs.miami.edu/SmallMolecules/)) [[data](http://zinc15.docking.org/catalogs/lincs/)]
+* [X] Prestwick Chemical Library `prestwick`: A commercial collection of over 1.2k off-patent drugs [[data](http://zinc15.docking.org/catalogs/prestwick/)]
+* [X] NIH Clinical Collection `nihcc`: Screening library used at the National Institute of Health [[data](http://zinc15.docking.org/catalogs/nihcc/)]
+* [X] NCI Diversity Collection `ncidiv`: Screening library of the [Developmental Therapeutics Program](http://zinc15.docking.org/catalogs/ncidiv/) [[data](http://zinc15.docking.org/catalogs/ncidiv/)]
+* [X] Tool Compounds `toolcompounds`: Tool compounds according to [ZINC](http://zinc15.docking.org/) [[data](http://zinc15.docking.org/toolcompounds/)]
+
+## Chemogenomics libraries
+
+There is a large number number of chemogenomics databases that one may consider. I list here the ones selected in an important [recent review](https://www.nature.com/articles/nrd.2016.244) on the matter.
+
+* [ ] Pfizer chemogenomic library: Compound selection based on the most selective pharmacological probe for a given target, and maximal chemical and biological diversity;
+dominated by kinases, GPCRs and ion channels; available for external collaboration.
+* [ ] Sigma library of pharmacologically active compounds (LOPAC1280): Commercially available, widely reported, well suited for GPCR biology.
+* [ ] Prestwick Chemical Library (see above): Contains only approved drugs.
+* [ ] GlaxoSmithKline Biologically Diverse Compound Set: Selective pharmacological probes, dominated by kinase and GPCR targets.
+* [ ] Mechanism Interrogation PlatE 3.0 (NCATS): Oncology focused and dominated by kinase inhibitors. Well suited for anticancer screens.
+* [ ] NIH Molecular Libraries Program Probes: Good coverage of nucleic acid-binding proteins; all bioassay data are open access.
+* [ ] GlaxoSmithKline Protein Kinase Inhibitor Set: Open source kinase chemical probes. 
 
 ## Natural product databases
 
 We have a particular interest in natural product (NP) databases, mainly because they are likely to be useful for Global Health research.
 
-* South African Natural Compounds Database (SANCDB): [https://sancdb.rubi.ru.ac.za/](https://sancdb.rubi.ru.ac.za/). Contains about 600 NPs, all of them with some degree of bioactivity annotation. Belongs to the Research Unit in Bioinformatics (RUBi), NIH Common Fund and Rhodes University.
-
-* AfroDB: [Dataset 1 in Ntie-Kang et al. 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078085#s5). Contains 947 compounds. Coordinated from Cameroon.
-
-* Natural Product Activity and Species Source database (NPASS): [http://bidd2.nus.edu.sg/NPASS/](http://bidd2.nus.edu.sg/NPASS/). Over 35k well-annotated compounds, belonging to 25k organisms.
-
-* Northern African Natural Products Database (NANPDB): [http://african-compounds.org/nanpdb/](http://african-compounds.org/nanpdb/). About 4.5k NPs from Northern Africa, mainly from plants.
-
-* Brazilian Natural Compound Database (NUBBEdb): [https://nubbe.iq.unesp.br/portal/nubbedb.html](https://nubbe.iq.unesp.br/portal/nubbedb.html). Contains 640 molecules mainly from plants in Brazil.
+* [ ] [South African Natural Compounds Database](https://sancdb.rubi.ru.ac.za/) (SANCDB): Contains about 600 NPs, all of them with some degree of bioactivity annotation. Belongs to the Research Unit in Bioinformatics (RUBi), NIH Common Fund and Rhodes University.
+* [ ] AfroDB: [Dataset 1 in Ntie-Kang et al. 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078085#s5). Contains 947 compounds. Coordinated from Cameroon.
+* [ ] Natural Product Activity and Species Source database (NPASS): [http://bidd2.nus.edu.sg/NPASS/](http://bidd2.nus.edu.sg/NPASS/). Over 35k well-annotated compounds, belonging to 25k organisms.
+* [ ] [Northern African Natural Products Database](http://african-compounds.org/nanpdb/) (NANPDB): About 4.5k NPs from Northern Africa, mainly from plants.
+* [ ] [Brazilian Natural Compound Database](https://nubbe.iq.unesp.br/portal/nubbedb.html) (NUBBEdb): Contains 640 molecules mainly from plants in Brazil.