knit

README.md

@@ -3,96 +3,81 @@
 
 # The dynamic landscape of peptide function prediction
 
-This curated list collects peer-reviewed machine learning models
-dedicated to predicting specific properties of peptides. For an
-interactive and browse-able list, please visit:
-<https://biogenies.info/peptide-prediction-list/>.
+<!-- This curated list collects peer-reviewed machine learning models dedicated to predicting specific properties of peptides.  -->
+
+For an interactive and browse-able list, please visit:
+<https://biogenies.info/amyloid-database-list/>.
 
 - [Active](#active)
 - [Non-active](#non-active)
 
 ## Active
 
-1.  A3D-MODB:
-    [publication](https://doi.org/https://doi.org/10.1093/nar/gkad942);
+1.  A3D-MODB: [publication](https://doi.org/10.1093/nar/gkad942);
     [database](https://biocomp.chem.uw.edu.pl/A3D2/MODB).
-2.  AL-Base:
-    [publication](https://doi.org/https://doi.org/10.1080/13506120802676781);
+2.  AL-Base: [publication](https://doi.org/10.1080/13506120802676781);
     [database](https://wwwapp.bumc.bu.edu/BEDAC_ALBase/).
 3.  AmyLoad:
-    [publication](https://doi.org/https://doi.org/10.1093/bioinformatics/btv375);
+    [publication](https://doi.org/10.1093/bioinformatics/btv375);
     [database](http://comprec-lin.iiar.pwr.edu.pl/amyload/).
-4.  AmyloBase:
-    [publication](https://doi.org/https://doi.org/10.1038%2Fembor.2011.116);
+4.  AmyloBase: [publication](https://doi.org/10.1038%2Fembor.2011.116);
     [database](http://bioserver2.sbsc.unifi.it/AmyloBase.html).
-5.  AmyloGraph:
-    [publication](https://doi.org/https://doi.org/10.1093/nar/gkac882);
+5.  AmyloGraph: [publication](https://doi.org/10.1093/nar/gkac882);
     [database](http://amylograph.com/).
 6.  Amyloid Atlas 2024:
-    [publication](https://doi.org/https://doi.org/10.1016/j.cell.2021.08.013);
+    [publication](https://doi.org/10.1016/j.cell.2021.08.013);
     [database](https://people.mbi.ucla.edu/sawaya/amyloidatlas/).
-7.  AmyPro:
-    [publication](https://doi.org/https://doi.org/10.1093/nar/gkx950);
+7.  AmyPro: [publication](https://doi.org/10.1093/nar/gkx950);
     [database](http://amypro.net).
-8.  CARs DB:
-    [publication](https://doi.org/https://doi.org/10.1007/978-1-0716-3441-7_10);
+8.  CARs DB: [publication](https://doi.org/10.3389/fmolb.2022.882160);
     [database](http://carsdb.ppmclab.com/).
-9.  CPAD2:
-    [publication](https://doi.org/https://doi.org/10.1080/13506129.2020.1715363);
+9.  CPAD2: [publication](https://doi.org/10.1080/13506129.2020.1715363);
     [database](https://web.iitm.ac.in/bioinfo2/cpad2/index.html).
 10. Cross-Beta DB:
-    [publication](https://doi.org/https://doi.org/10.1101/2024.02.12.579644);
+    [publication](https://doi.org/10.1101/2024.02.12.579644);
     [database](https://crossbetadb.crbm.cnrs.fr/).
 11. Fibrilizer:
-    [publication](https://doi.org/http://dx.doi.org/10.1016/j.bpj.2012.12.037);
+    [publication](http://dx.doi.org/10.1016/j.bpj.2012.12.037);
     [database](https://amyloid.cs.mcgill.ca/database/index.html).
-12. PrionScan:
-    [publication](https://doi.org/https://doi.org/10.1186/1471-2164-15-102);
+12. PrionScan: [publication](https://doi.org/10.1186/1471-2164-15-102);
     [database](http://webapps.bifi.es/prionscan).
 13. SAPdb:
-    [publication](https://doi.org/https://doi.org/10.1016/j.compbiomed.2021.104391);
+    [publication](https://doi.org/10.1016/j.compbiomed.2021.104391);
     [database](https://webs.iiitd.edu.in/raghava/sapdb/).
 14. StAmP:
-    [publication](https://doi.org/https://doi.org/10.1093/bioinformatics/btac126);
+    [publication](https://doi.org/10.1093/bioinformatics/btac126);
     [database](https://stamp.switchlab.org/).
-15. Waltz DB 2.0:
-    [publication](https://doi.org/https://doi.org/10.1093/nar/gkz758);
+15. Waltz DB 2.0: [publication](https://doi.org/10.1093/nar/gkz758);
     [database](http://waltzdb.switchlab.org/).
 
 ## Non-active
 
-1.  AmyCo:
-    [publication](https://doi.org/https://doi.org/10.1080/13506129.2019.1603143);
+1.  AmyCo: [publication](https://doi.org/10.1080/13506129.2019.1603143);
     [database](http://bioinformatics.biol.uoa.gr/amyco).
 2.  amyloid interactome:
-    [publication](https://doi.org/https://doi.org/10.1371/journal.pone.0173163);
+    [publication](https://doi.org/10.1371/journal.pone.0173163);
     [database](http://83.212.109.111/amyloid_interactome).
 3.  Amyloïdose gezamenlijk:
-    [publication](https://doi.org/https://doi.org/10.3109/13506129.2014.964858);
+    [publication](https://doi.org/10.3109/13506129.2014.964858);
     [database](http://www.amyloidosis.nl/).
-4.  AmyPDB:
-    [publication](https://doi.org/https://doi.org/10.1186/1471-2105-9-273);
+4.  AmyPDB: [publication](https://doi.org/10.1186/1471-2105-9-273);
     [database](http://amypdb.genouest.org/;%20https://amypdb.univ-rennes1.fr/).
-5.  fibril_one:
-    [publication](https://doi.org/https://doi.org/10.1110%2Fps.0204302);
+5.  fibril_one: [publication](https://doi.org/10.1110%2Fps.0204302);
     [database](http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one).
-6.  pE-DB:
-    [publication](https://doi.org/https://doi.org/10.1093/nar/gkt960);
+6.  pE-DB: [publication](https://doi.org/10.1093/nar/gkt960);
     [database](https://pedb.vib.be/).
 7.  PrionHome:
-    [publication](https://doi.org/https://doi.org/10.1371/journal.pone.0031785);
+    [publication](https://doi.org/10.1371/journal.pone.0031785);
     [database](https://libaio.biol.mcgill.ca/prion).
-8.  ProADD:
-    [publication](https://doi.org/https://doi.org/10.6026%2F97320630010390);
+8.  ProADD: [publication](https://doi.org/10.6026%2F97320630010390);
     [database](http://bicmku.in/ProADD).
 9.  The Prion Disease Database:
-    [publication](https://doi.org/https://doi.org/10.1093/database/bap011);
+    [publication](https://doi.org/10.1093/database/bap011);
     [database](http://prion.systemsbiology.net).
 10. THERPA v2:
-    [publication](https://doi.org/http://dx.doi.org/10.1080/19336896.2019.1689789);
+    [publication](http://dx.doi.org/10.1080/19336896.2019.1689789);
     [database](http://www.nih.go.kr/therpa%20;%20https://therpa.pythonanywhere.com/).
-11. ZipperDB:
-    [publication](https://doi.org/https://doi.org/10.1073/pnas.0915166107);
+11. ZipperDB: [publication](https://doi.org/10.1073/pnas.0915166107);
     [database](https://services.mbi.ucla.edu/zipperdb/intro).
 
 ### About and citation

docs/index.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(echo = FALSE)
 
 library(DT)
 library(dplyr)
+library(stringr)
 
 dat <- readr::read_csv("../data/amyloid_db.csv", col_select = c(, 1:14), col_types = "fcfffffff?cccf") %>% 
   # filter(`Current status` == "Active") %>%