Protein dna docking tutorial with haddock3

Gemfile.lock

@@ -0,0 +1,145 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    colorator (1.1.0)
+    concurrent-ruby (1.3.4)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    eventmachine (1.2.7)
+    ffi (1.17.0)
+    ffi (1.17.0-aarch64-linux-gnu)
+    ffi (1.17.0-aarch64-linux-musl)
+    ffi (1.17.0-arm-linux-gnu)
+    ffi (1.17.0-arm-linux-musl)
+    ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86-linux-gnu)
+    ffi (1.17.0-x86-linux-musl)
+    ffi (1.17.0-x86_64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
+    ffi (1.17.0-x86_64-linux-musl)
+    forwardable-extended (2.6.0)
+    google-protobuf (3.25.4)
+    google-protobuf (3.25.4-aarch64-linux)
+    google-protobuf (3.25.4-arm64-darwin)
+    google-protobuf (3.25.4-x86-linux)
+    google-protobuf (3.25.4-x86_64-darwin)
+    google-protobuf (3.25.4-x86_64-linux)
+    http_parser.rb (0.8.0)
+    i18n (1.14.5)
+      concurrent-ruby (~> 1.0)
+    jekyll (4.3.3)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 2.3, >= 2.3.1)
+      kramdown-parser-gfm (~> 1.0)
+      liquid (~> 4.0)
+      mercenary (>= 0.3.6, < 0.5)
+      pathutil (~> 0.9)
+      rouge (>= 3.0, < 5.0)
+      safe_yaml (~> 1.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
+    jekyll-feed (0.17.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    kramdown (2.4.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    mercenary (0.4.0)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (6.0.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    rexml (3.3.5)
+      strscan
+    rouge (4.3.0)
+    safe_yaml (1.0.5)
+    sass-embedded (1.69.5-aarch64-linux-android)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-aarch64-linux-gnu)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-aarch64-linux-musl)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-arm-linux-androideabi)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-arm-linux-gnueabihf)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-arm-linux-musleabihf)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-arm64-darwin)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86-linux-android)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86-linux-gnu)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86-linux-musl)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86_64-darwin)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86_64-linux-android)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86_64-linux-gnu)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86_64-linux-musl)
+      google-protobuf (~> 3.23)
+    strscan (3.1.0)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    unicode-display_width (2.5.0)
+    webrick (1.8.1)
+
+PLATFORMS
+  aarch64-linux
+  aarch64-linux-android
+  aarch64-linux-gnu
+  aarch64-linux-musl
+  arm-linux-androideabi
+  arm-linux-gnu
+  arm-linux-gnueabihf
+  arm-linux-musl
+  arm-linux-musleabihf
+  arm64-darwin
+  x86-linux
+  x86-linux-android
+  x86-linux-gnu
+  x86-linux-musl
+  x86_64-darwin
+  x86_64-linux
+  x86_64-linux-android
+  x86_64-linux-gnu
+  x86_64-linux-musl
+
+DEPENDENCIES
+  http_parser.rb (~> 0.6.0)
+  jekyll (~> 4.3.2)
+  jekyll-feed (~> 0.12)
+  minima (~> 2.5)
+  tzinfo (>= 1, < 3)
+  tzinfo-data
+  wdm (~> 0.1.1)
+
+BUNDLED WITH
+   2.5.17

education/HADDOCK3/index.md

@@ -25,3 +25,9 @@ _Note that HADDOCK3 is still in heavy development and as such the software is ev
   This tutorial demonstrates the use of HADDOCK3 for predicting the structure of an antibody-antigen complex using information
   about the hypervariable loops of the antibody and a loose definition of the epitope determined through NMR experiments.
   As HADDOCK3 only exists as a command line version, this tutorial does require some basic Linux expertise.
+
+* [**HADDOCK3 basic protein-DNA docking tutorial**](/education/HADDOCK3/HADDOCK3-protein-DNA-basic):
+  This tutorial demonstrates the use of HADDOCK3 for predicting the structure of a protein-DNA complex in which two protein units 
+  bind to the double-stranded DNA in a symmetrical manner (3CRO). Next to provided ambiguous restraints to drive the docking symmetry 
+  restraints are defined to enforce symmetrical protein binding. As HADDOCK3 only exists as a command line version, this tutorial does
+  require some basic Linux expertise.