another update

README.md

@@ -14,22 +14,17 @@ For an interactive and browse-able list, please visit:
 
 ## Experimental
 
-1.  AL-Base: [publication](https://doi.org/10.1080/13506120802676781);
-    [database](https://wwwapp.bumc.bu.edu/BEDAC_ALBase/).
-2.  AmyloBase: [publication](https://doi.org/10.1038%2Fembor.2011.116);
+1.  AmyloBase: [publication](https://doi.org/10.1038%2Fembor.2011.116);
     [database](http://bioserver2.sbsc.unifi.it/AmyloBase.html).
-3.  AmyloGraph: [publication](https://doi.org/10.1093/nar/gkac882);
+2.  AmyloGraph: [publication](https://doi.org/10.1093/nar/gkac882);
     [database](http://amylograph.com/).
-4.  Amyloid Atlas:
+3.  Amyloid Atlas:
     [publication](https://doi.org/10.1016/j.cell.2021.08.013);
     [database](https://people.mbi.ucla.edu/sawaya/amyloidatlas/).
-5.  AmyPro: [publication](https://doi.org/10.1093/nar/gkx950);
+4.  AmyPro: [publication](https://doi.org/10.1093/nar/gkx950);
     [database](http://amypro.net).
-6.  CPAD2: [publication](https://doi.org/10.1080/13506129.2020.1715363);
+5.  CPAD2: [publication](https://doi.org/10.1080/13506129.2020.1715363);
     [database](https://web.iitm.ac.in/bioinfo2/cpad2/index.html).
-7.  SAPdb:
-    [publication](https://doi.org/10.1016/j.compbiomed.2021.104391);
-    [database](https://webs.iiitd.edu.in/raghava/sapdb/).
 
 ## Prediction
 

docs/index.Rmd

@@ -131,19 +131,26 @@ To collect amyloid-related databases, we searched PubMed, Google and Google Scho
 We manually curated all information for databases featured in a **Amyloid-related database list** tab. To do that we carefully analysed publications and/or websites describing given database looking for the following information:
 
 - link to the web server (integrated into **Database name** column),
-- link to the paper (if applicable) (**DOI** column),
-- external sources of proteins/peptides in database (we didn't mention own discoveries) and links to and other sources that are integrated into the database (**Data sources and links to other db** column).
-- what kind of data do they store (**Type of data** column)
-- current status of database (**Current status**)
-
-Then, we checked if the links to the databases provided in the articles were still working and if they function correctly. Otherwise, we tried to find the link either through a search engine search or by contacting the database developers. 
+- what is their focus, amyloids, prions, IDPs, interactions (**Focus** column)
+- what kind of data do they store, experimental, predictions or both (**Type of data** column)
+- do they store only amyloids (**Only amyloids** column)
+- do they include experimental conditions (**Includes experimental conditions** column)
+- usability of data creating generalized models (**Usability** column),
+- what kind of structural information is gathered (*Includes structural information** column),
+- do they highlight proteins APRs (**Identifies APRs** column),
+- current status of database (**Current status**),
+- date of last update or publication date (**Last updated** column),
+- external sources of proteins/peptides in database (we didn't mention own discoveries) and links to and other sources that are integrated into the database (**Data sources and links to other db** column),
+- link to publication (**DOI** column)
+
+Then, we checked if the links to the databases provided in the articles function correctly. Otherwise, we tried to find them either through a search engine or by contacting the database developers. 
 
 The **Updates** tab indicates latest changes in the list.
 
 
 ### Updates
 
-**30/07/2024** - first release
+**17/07/2024** - first release
 
 
 ### About and citation