Review website content (DS)

.github/workflows/ci.yaml

@@ -30,7 +30,7 @@ jobs:
       - name: Build & check
         run: |
           hugo
-          npx linkinator ./public --recurse --retry --timeout=5000 --skip \
+          npx linkinator ./public --recurse --retry --timeout=5000 --concurrency 50 --skip \
             'https://github.com/volkamerlab/CADDCourse2020,
              https://github.com/volkamerlab/CADDSeminar_2020,
              https://github.com/volkamerlab/CADDSeminar_2019,
@@ -40,6 +40,9 @@ jobs:
              https://dx.doi.org/10.1007/s10822-020-00310-4,
              https://www.einsteinfoundation.de/en/people-projects/einstein-bih-visiting-fellows/john-chodera/,
              https://www.einsteinfoundation.de/en/programmes/einstein-bih-visiting-fellow/,
+             https://systemsbiology.columbia.edu/faculty/mohammed-alquraishi,
+             https://systemsbiology.columbia.edu/,
+             https://www.bayer.com/,
              linkedin.com,
              html5up.net,
              gepris.dfg.de,

content/education/ai-in-medicine.md

@@ -19,4 +19,4 @@ The goal of this course (_Wahlpflichtmodul M24_) is to familiarize medical stude
 
 ## Resources
 
-* <a class="icon fa-lock" target="_blank" href="https://github.com/volkamerlab/ai_in_medicine" title="Access restricted to enrolled students"> AI in Medicine repository (2020)</a>
+* <a class="icon fa-github" target="_blank" href="https://github.com/volkamerlab/ai_in_medicine" title="AI in Medicine repository"> AI in Medicine repository</a>

content/projects/kinfraglib.md

@@ -38,3 +38,4 @@ in order to generate potential novel inhibitors.
 
 
 {{< xfigure src="/images/research/kinfraglib.png" caption="Ligands co-crystalized with kinases are fragmented with respect to important kinase subpockets, resulting in a kinase-focused fragment library (*KinFragLib*) used for chemical space analysis and recombination." imageclass="fit" >}}
+

content/projects/kissim.md

@@ -17,7 +17,7 @@ collaborators:
 external_resources:
 - name: kissim
   link: https://github.com/volkamerlab/kissim
-  icon: lock
+  icon: github
   more: Subpocket-based fingerprint for structural kinase comparison (WIP)
 funding:
 - name: Bundesministerium für Bildung und Forschung, grant ID 031A262C
@@ -29,7 +29,7 @@ Kinases are important and well studied drug targets for cancer and inflammatory
 Due to the highly conserved structure of kinases, especially at the ATP binding site,
 the main challenge when developing kinase inhibitors is achieving selectivity,
 which requires a comprehensive understanding of kinase similarity.
-In our *KiSSim* (kinase structural similarity) project, we developed a subpocket-focused kinase fingerprint to investigate kinome-wide pocket similarity.
+In our *KiSSim* (Kinase Structural Similarity) project, we developed a subpocket-focused kinase fingerprint to investigate kinome-wide pocket similarity.
 
 <!--more-->
 

content/projects/opencadd.md

@@ -6,12 +6,13 @@ draft: false
 people:
   - key: jaime.rodriguez
   - key: dominique.sydow
+  - key: julian.pipart
   - key: andrea.volkamer
 collaborators:
   - name: Dennis Köser, Annie Pham, Enes Kurnaz, Julian Pipart
     more: Structural Alignment 2020 (FU)
-  - name: Franzis Fritz
-    more: Protein-ligand interaction fingerprints
+  - name: Julian Pipart, Corey Taylor
+    more: Benchmarking OpenCADD's structural superposition tool, bachelor thesis 2021 (FU)
 external_resources:
   - name: OpenCADD repository
     link: https://github.com/volkamerlab/opencadd
@@ -29,3 +30,9 @@ OpenCADD is a Python library for structural cheminformatics.
 <!--more-->
 
 {{< xfigure src="/images/research/opencadd.png" imageclass="fit" caption="The logo of the OpenCADD project." >}}
+
+OpenCADD is a collection of independent Python modules:
+
+- ``structure.superposition``: superimpose macromolecules using sequence and structural information.
+- ``structure.pocket``: define and visualize protein (sub)pockets.
+- ``databases.klifs``: query the [KLIFS](https://klifs.net/) database, offline or online.

content/projects/ratar.md

@@ -21,7 +21,7 @@ publications:
 ---
 
 How to probe and validate a potential target remains one of the key questions in basic research in life sciences.
-In the DFG-project "Read-Across the Targetome" (*Ratar*), we will use binding site similarity to predict off-targets and
+In the DFG-project *Ratar* (Read-Across the Targetome), we will use binding site similarity to predict off-targets and
 to extrapolate compound information from one target to another.
 This similarity-based knowledge transfer can suggest tool compounds (chemical probes) and
 off-targets for proteins of interest using the ever-growing amount of available target and compound data.

content/projects/t2f-flex.md

@@ -19,7 +19,3 @@ T²F-Flex extends the functionality of [T²F-Pharm](/projects/t2f-pharm) and off
 Interaction hotspots on the grid are calculated per snapshot (subset of the trajectory) and subsequently clustered and summarized into a single pharmacophore model.
 This method allows to generate pharmacophores in the absence of ligand
 or interaction information and provides a feature-based description of protein binding sites.
-
-<!--more-->
-
-Work on this project is ongoing in the Master thesis of [Michele Wichmann](/team/#michele.wichmann).

content/projects/teachopencadd.md

@@ -8,35 +8,45 @@ menu:
     main:
         parent: Education
 external_resources:
+- name: TeachOpenCADD website
+  link: https://projects.volkamerlab.org/teachopencadd/
+  icon: globe
+  more: Main website for the TeachOpenCADD platform
 - name: TeachOpenCADD for Jupyter
   link: https://github.com/volkamerlab/TeachOpenCADD
   icon: github
   more: Jupyter notebooks on computer-aided drug design tasks using open resources
 - name: TeachOpenCADD for KNIME
   link: https://hub.knime.com/volkamerlab/spaces/Public/latest/TeachOpenCADD/TeachOpenCADD
+  icon: globe
   more: KNIME workflows on computer-aided drug design tasks using open resources
 people:
+# List here everyone who co-authored TOC publications and is/was a Volkamer Lab member
 - key: dominique.sydow
 - key: jaime.rodriguez
+- key: andrea.volkamer
+- key: talia.kimber
+- key: david.schaller
+- key: corey.taylor
+- key: yonghui.chen
 - key: michele.wichmann
+- key: mareike.leja
+- key: sakshi.misra
 - key: andrea-lilian.morger
 - key: maximilian.driller
-- key: andrea.volkamer
+- key: Armin Ariamajd
 collaborators:
+# List here everyone who co-authored TOC publications outside of the Volkamer Lab
 - name: Greg Landrum
   more: KNIME
 - name: Daria Goldmann
   more: KNIME
 funding:
-- name: Bundesministerium für Bildung und Forschung, grant ID 031A262C
-- name: Deutsche Forschungsgemeinschaft (DFG), grant ID VO 2353 / 1-1
-- name: HaVo-Stiftung, Ludwig-shafen, Germany
-- name: Open Access Publication Fund of Charité – Universitätsmedizin Berlin
-- name: Stiftung Charité (Einstein BIH Visiting Fellow Project)
-- name: “SUPPORT für die Lehre” program (Förderung innovativer Lehrvorhaben) of Freie Universität Berlin.
+- name: Note that the TeachOpenCADD project has been a group effort and has received no explicit funding, while the positions of individual authors were supported by diverse funding agencies, see the individual projects' pages.
 publications:
 - teachopencaddknime
 - teachopencadd
+- sydow_acs_2021
 # You can use this keyword for the brief introductions to the article in category listings
 # This will replace the first 70 words found in the main article. use | <newline> to use multiline strings!
 summary: |
@@ -63,33 +73,4 @@ TeachOpenCADD is suitable for self-study training and classroom teaching, but ca
 research projects.
 The platform is freely available on GitHub and open to contributions from the community.
 
-{{< xfigure src="/images/research/teachopencadd_topics1-10.png" caption="The TeachOpenCADD platform offers tutorials covering a step-by-step pipeline to propose novel EGFR kinase inhibitors with concepts from cheminformatics (green) and structural bioinformatics (orange)." imageclass="fit" >}}
-
-### TeachOpenCADD topics
-
-TeachOpenCADD offers teaching material on common tasks in computer-aided drug design. Currently, the following topics are available:
-
-##### Cheminformatics
-
-1. Compound data acquisition: ChEMBL
-2. Molecular filtering: ADME and lead-likeness criteria
-3. Molecular filtering: Unwanted substructures
-4. Ligand-based screening: Compound similarity
-5. Compound clustering
-6. Maximum common substructures
-7. Ligand-based screening: Machine learning
-
-##### Structural bioinformatics
-
-8. Protein data acquisition: Protein Data Bank (PDB)
-9. Ligand-based pharmacophores
-10. Binding site similarity
-
-<!-- 11. Structure-based CADD using online APIs/servers -->
-<!-- * Querying KLIFS & PubChem for potential kinase inhibitors -->
-<!-- * Docking the candidates against the target -->
-<!-- * Visualizing the results and comparing against known data -->
-
-<!-- {{< xfigure src="/images/research/teachopencadd_topics11.png" caption="Topic 11" >}} -->
-
-Topics 1-10 are available as Python-based Jupyter notebooks and topics 1-8 can additionally be used in the form of KNIME workflows.
+{{< xfigure src="/images/research/teachopencadd.png" caption="The TeachOpenCADD platform offers tutorials covering a step-by-step pipeline to propose novel EGFR kinase inhibitors with concepts from cheminformatics (green), structural bioinformatics (orange), and online webserver queries (blue)." imageclass="fit" >}}

content/research/structure-based/binding-sites.md

@@ -1,5 +1,5 @@
 ---
-title: Binding-site comparison
+title: Binding site comparison
 date: 2020-03-03
 publishdate: 2020-03-03
 weight: 10