From f1a4c1860b7fc28ea96ae76ae169a83071a4fcf8 Mon Sep 17 00:00:00 2001
From: jarochi <jaroslaw.chilimoniuk@gmail.com>
Date: Thu, 18 Jul 2024 23:07:09 +0200
Subject: [PATCH] knit

---
 README.md       | 75 ++++++++++++++++++++-----------------------------
 docs/index.Rmd  |  1 +
 docs/index.html |  4 +--
 3 files changed, 33 insertions(+), 47 deletions(-)

diff --git a/README.md b/README.md
index 33d9024..cb5e172 100644
--- a/README.md
+++ b/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
diff --git a/docs/index.Rmd b/docs/index.Rmd
index d6cc93d..f0f5202 100644
--- a/docs/index.Rmd
+++ b/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") %>% 
diff --git a/docs/index.html b/docs/index.html
index 06b109a..280d15f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -3416,8 +3416,8 @@ <h1 class="title toc-ignore">Amyloid databases list</h1>
 <h2 class="tabset"></h2>
 <div id="software-information" class="section level3">
 <h3>Software information</h3>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-a38def01fc17c26a64c8" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-a38def01fc17c26a64c8">{"x":{"style":"bootstrap","filter":"top","vertical":false,"filterHTML":"<tr>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","extensions":["Buttons","FixedColumns","FixedHeader"],"data":[["Amyloid Atlas 2024","CARs DB","AmyloGraph","AL-Base","Waltz DB 2.0","CPAD2","StAmP","AmyLoad","AmyPro","A3D-MODB","Cross-Beta DB","SAPdb","Fibrilizer","ZipperDB","PrionScan","pE-DB","AmyPDB","ProADD","AmyCo","fibril_one","AmyloBase","Amyloïdose gezamenlijk","amyloid interactome","PrionHome","THERPA v2","The Prion Disease Database"],["<a href='https://doi.org/10.1016/j.cell.2021.08.013' >https://doi.org/10.1016/j.cell.2021.08.013<\/a>","<a href='https://doi.org/10.1007/978-1-0716-3441-7_10' >https://doi.org/10.1007/978-1-0716-3441-7_10<\/a>","<a href='https://doi.org/10.1093/nar/gkac882' >https://doi.org/10.1093/nar/gkac882<\/a>","<a href='https://doi.org/10.1080/13506120802676781' >https://doi.org/10.1080/13506120802676781<\/a>","<a href='https://doi.org/10.1093/nar/gkz758' >https://doi.org/10.1093/nar/gkz758<\/a>","<a href='https://doi.org/10.1080/13506129.2020.1715363' >https://doi.org/10.1080/13506129.2020.1715363<\/a>","<a href='https://doi.org/10.1093/bioinformatics/btac126' >https://doi.org/10.1093/bioinformatics/btac126<\/a>","<a href='https://doi.org/10.1093/bioinformatics/btv375' >https://doi.org/10.1093/bioinformatics/btv375<\/a>","<a href='https://doi.org/10.1093/nar/gkx950' >https://doi.org/10.1093/nar/gkx950<\/a>","<a href='https://doi.org/10.1093/nar/gkad942' >https://doi.org/10.1093/nar/gkad942<\/a>","<a href='https://doi.org/10.1101/2024.02.12.579644' >https://doi.org/10.1101/2024.02.12.579644<\/a>","<a href='https://doi.org/10.1016/j.compbiomed.2021.104391' >https://doi.org/10.1016/j.compbiomed.2021.104391<\/a>","<a href='http://dx.doi.org/10.1016/j.bpj.2012.12.037' >http://dx.doi.org/10.1016/j.bpj.2012.12.037<\/a>","<a href='https://doi.org/10.1073/pnas.0915166107' >https://doi.org/10.1073/pnas.0915166107<\/a>","<a href='https://doi.org/10.1186/1471-2164-15-102' >https://doi.org/10.1186/1471-2164-15-102<\/a>","<a href='https://doi.org/10.1093/nar/gkt960' >https://doi.org/10.1093/nar/gkt960<\/a>","<a href='https://doi.org/10.1186/1471-2105-9-273' >https://doi.org/10.1186/1471-2105-9-273<\/a>","<a href='https://doi.org/10.6026%2F97320630010390' >https://doi.org/10.6026%2F97320630010390<\/a>","<a href='https://doi.org/10.1080/13506129.2019.1603143' >https://doi.org/10.1080/13506129.2019.1603143<\/a>","<a href='https://doi.org/10.1110%2Fps.0204302' >https://doi.org/10.1110%2Fps.0204302<\/a>","<a href='https://doi.org/10.1038%2Fembor.2011.116' >https://doi.org/10.1038%2Fembor.2011.116<\/a>","<a href='https://doi.org/10.3109/13506129.2014.964858' >https://doi.org/10.3109/13506129.2014.964858<\/a>","<a href='https://doi.org/10.1371/journal.pone.0173163' >https://doi.org/10.1371/journal.pone.0173163<\/a>","<a href='https://doi.org/10.1371/journal.pone.0031785' >https://doi.org/10.1371/journal.pone.0031785<\/a>","<a href='http://dx.doi.org/10.1080/19336896.2019.1689789' >http://dx.doi.org/10.1080/19336896.2019.1689789<\/a>","<a href='https://doi.org/10.1093/database/bap011' >https://doi.org/10.1093/database/bap011<\/a>"],["<a href='https://people.mbi.ucla.edu/sawaya/amyloidatlas/' > link <\/a>","<a href='http://carsdb.ppmclab.com/' > link <\/a>","<a href='http://amylograph.com/' > link <\/a>","<a href='https://wwwapp.bumc.bu.edu/BEDAC_ALBase/' > link <\/a>","<a href='http://waltzdb.switchlab.org/' > link <\/a>","<a href='https://web.iitm.ac.in/bioinfo2/cpad2/index.html' > link <\/a>","<a href='https://stamp.switchlab.org/' > link <\/a>","<a href='http://comprec-lin.iiar.pwr.edu.pl/amyload/' > link <\/a>","<a href='http://amypro.net' > link <\/a>","<a href='https://biocomp.chem.uw.edu.pl/A3D2/MODB' > link <\/a>","<a href='https://crossbetadb.crbm.cnrs.fr/' > link <\/a>","<a href='https://webs.iiitd.edu.in/raghava/sapdb/' > link <\/a>","<a href='https://amyloid.cs.mcgill.ca/database/index.html' > link <\/a>","<a href='https://services.mbi.ucla.edu/zipperdb/intro' > link <\/a>","<a href='http://webapps.bifi.es/prionscan' > link <\/a>","<a href='https://pedb.vib.be/' > link <\/a>","<a href='http://amypdb.genouest.org/; https://amypdb.univ-rennes1.fr/' > link <\/a>","<a href='http://bicmku.in/ProADD' > link <\/a>","<a href='http://bioinformatics.biol.uoa.gr/amyco' > link <\/a>","<a href='http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one' > link <\/a>","<a href='http://bioserver2.sbsc.unifi.it/AmyloBase.html' > link <\/a>","<a href='http://www.amyloidosis.nl/' > link <\/a>","<a href='http://83.212.109.111/amyloid_interactome' > link <\/a>","<a href='https://libaio.biol.mcgill.ca/prion' > link <\/a>","<a href='http://www.nih.go.kr/therpa ; https://therpa.pythonanywhere.com/' > link <\/a>","<a href='http://prion.systemsbiology.net' > link <\/a>"],["Amyloids","IDP regions","interactions","Amyloids","Amyloids","Amyloids","Amyloids","Amyloids","Amyloids","Amyloids","Amyloids","other","Amyloids","Amyloids","Prion",null,null,null,null,null,"Amyloids",null,null,"Prion",null,"Prion"],["Experimental","Prediction","Experimental","Experimental","both","Experimental","both","both","Experimental","Prediction","both","Experimental","Prediction","Prediction","Prediction",null,null,null,null,null,"Experimental",null,null,"both",null,"Experimental"],["No","No","No","No","Yes","Yes","No","Yes","No","No","Yes","Yes","No","No","No",null,null,null,null,null,"Yes",null,null,"Yes",null,"Yes"],["General","General","General","Specific","General","General","General","General","General","General","General","Specific","Specific","General","General",null,null,null,null,null,"General",null,null,"General",null,"Specific"],["Structure for the wt protein and the aggregate","Sequence-only","Sequence-only","Sequence-only","Structure for the wt protein and the aggregate","Structure for the wt protein","Sequence-only","Sequence-only","Structure for the wt protein","Structure for the wt protein and the aggregate","Structure for the wt protein","Structure for the wt protein","Structure for the wt protein","Structure for the wt protein and the aggregate","Sequence-only",null,null,null,null,null,"Sequence-only",null,null,"Structure for the wt protein",null,"Sequence-only"],["No","APRs","No","No","APRs","APRs","APRs","No","APRs","STAPs","APRs","STAPs","No","APRs","APRs",null,null,null,null,null,"No",null,null,"No",null,"No"],["PDB","DisProt, UniProt, Waltz","PubMed","NCBI","PubMed, Uniprot","CPAD, Waltz, AmyLoad, AmyPro, UniProt, PDB","PDB, Uniprot","TANGO, Waltz, AmylFrag, Aggrescan, AmylHex,","PDB, Uniprot, PubMed",null,"PDB, AmyPro, Uniprot, 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