Readme populated

README.md

@@ -1,3 +1,62 @@
 ---
 license: cc-by-4.0
+language:
+- en
+size_categories:
+- 10K<n<100K
 ---
+
+## Schema description:
+The manually curated dataset of open-closed monomers is included here as `benchmarking_monomeric_open_closed_conformers.csv`.  
+
+Column descriptions:
+
+## Schema description:
+The manually curated dataset of open-closed monomers is included here as `benchmarking_monomeric_open_closed_conformers.csv`.  
+
+Column descriptions:
+
+- **`UNP_ACC`** | UniProt accession code
+- **`UNP_START`** | Start of UniProt sequence for given PDBe entries
+- **`UNP_END`** | End of UniProt sequence for given PDBe entries
+- **`PDBe_ID`** | Protein Data Bank code
+- **`CHAIN_ID`**  | Author declared chain ID (`char`)
+- **`label_asym_id`** | Programmatically assigned chain ID (`char`)
+- **`CONFORMER_ID`** | Unique code for PDBe entries with distinct conformation, corresponding to a given UniProt accession
+- **`CONFORMER_DESCR`** | Short description of conformation, based on depositor's assessment of the protein/conformation
+- **`LIT_CONFIRMED`** | True/false value based on whether a publication (scientific literature) was available for manually curating clusters. NB: Clusters with 0 in this field should be used with caution. 
+-  **`ALT_CONFORMER_ID`** | Where the publication for a structure is currently outstanding, an executive decision on the conformation classification is made. Where the literature is not explicit on the features of a given conformation, the second most suitable `CONFORMER_ID` is provided in this column. Blank cells have no other likely conformation assignmnt and are therefore the same as in `CONFORMER_ID`. 
+- **`ALT_CONFORMER_DESCR`** | Description for conformation in alternative conformation ID. 
+
+## Curation process
+As of 09 Mar 2022, a manually curated dataset of monomeric protein conformations has been collated, containing 'open'-'closed' pairs as well as intermediary states defined by the authors of the entry. 
+
+1. The PDBe was queried, through its Oracle DB, to find PDBe entries with 100 % sequence identity for a UniProt segment in both 'open' and 'closed' conformations, as stated in the entry's `TITLE` field. The query used: 
+```
+select b.accession, b.unp_start, b.unp_end, a.id, a.title, d.id, d.title
+from entry a, unp_entity b, unp_entity c, entry d, pdb_assembly e
+where a.title like ‘%open%’  and d.title like ‘%close%’
+and a.id = b.entry_id and d.id = c.entry_id and a.id != d.id
+and b.accession = c.accession
+and b.unp_start = c.unp_start
+and b.unp_end = c.unp_end
+and a.id = e.entry_id
+and e.type = ‘homo’
+and e.name = ‘monomer’
+```
+was written by Dr Sameer Velankar. 
+
+2. These results were cleaned to remove entries with 'open' or 'close' substrings in their `TITLE`  fields that did not refer to conformation. The 'open' substring often appeared in ligand names in the entries' `TITLE` field, such as in *dichlorido(1,3-dimethylbenzimidaz ol-2-ylidene)(eta5-pentamethylcycl**open**tadienyl)rhodium(III)* and 'close' in terms like *dis**close**s*.
+
+3. All remaining entries were then manually curated by investigating each PDBe entry's corresponding publication, where available.
+ 1. Additional PDBe entries submitted by the authors, which were missed in the original search due to a lack of 'open' or 'close' substrings in their `TITLE` field but stated as fitting one of the states in the publication, were added.
+ 2. For some UniProt accessions, intermediary conformations were reported by the authors and these were noted in the dataset under the `CONFORMER_DESCR` column. 
+ 3. Entries deposited in monomeric form but solved as a multimeric complex were also removed. 
+
+4. PDBe entries, now clustered by author-stated conformation, were cross-referenced against the PDBe-KB's existing clustering algorithm (available on the [Aggregate Views of Proteins](https://www.ebi.ac.uk/pdbe/pdbe-kb/protein) page) to assess current conformer clustering success. These results are currently awaiting publication. 
+
+### Curation process outline
+<img src="http://ftp.ebi.ac.uk/pub/databases/pdbe-kb/benchmarking/distinct-monomer-conformers/work_progress_flowdiagram_200pc.png" alt="Curation flow diagram">
+
+### Dataset summary
+<img src="http://ftp.ebi.ac.uk/pub/databases/pdbe-kb/benchmarking/distinct-monomer-conformers/summary_data_visualisation.png" alt="Benchmark dataset summary graphs">