diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index fb05214..793e756 100644 --- a/.github/workflows/ci.yaml +++ b/.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, diff --git a/content/education/ai-in-medicine.md b/content/education/ai-in-medicine.md index 115f537..be7deda 100644 --- a/content/education/ai-in-medicine.md +++ b/content/education/ai-in-medicine.md @@ -19,4 +19,4 @@ The goal of this course (_Wahlpflichtmodul M24_) is to familiarize medical stude ## Resources -* AI in Medicine repository (2020) \ No newline at end of file +* AI in Medicine repository \ No newline at end of file diff --git a/content/projects/kinfraglib.md b/content/projects/kinfraglib.md index 325daa4..76007b4 100644 --- a/content/projects/kinfraglib.md +++ b/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" >}} + diff --git a/content/projects/kissim.md b/content/projects/kissim.md index 7a806b5..10f47b6 100644 --- a/content/projects/kissim.md +++ b/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. diff --git a/content/projects/opencadd.md b/content/projects/opencadd.md index 1e5905d..4a8c8ae 100644 --- a/content/projects/opencadd.md +++ b/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. {{< 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. diff --git a/content/projects/ratar.md b/content/projects/ratar.md index 17f5a2a..499b5f8 100644 --- a/content/projects/ratar.md +++ b/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. diff --git a/content/projects/t2f-flex.md b/content/projects/t2f-flex.md index bdda5c8..0756573 100644 --- a/content/projects/t2f-flex.md +++ b/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. - - - -Work on this project is ongoing in the Master thesis of [Michele Wichmann](/team/#michele.wichmann). \ No newline at end of file diff --git a/content/projects/teachopencadd.md b/content/projects/teachopencadd.md index 8d4d2e0..c8649fe 100644 --- a/content/projects/teachopencadd.md +++ b/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 | 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 - - - - - - - - -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" >}} diff --git a/content/research/structure-based/binding-sites.md b/content/research/structure-based/binding-sites.md index cca8904..453cbe8 100644 --- a/content/research/structure-based/binding-sites.md +++ b/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 diff --git a/static/images/research/kinfraglib.png b/static/images/research/kinfraglib.png index 168bf79..b6a8f45 100644 Binary files a/static/images/research/kinfraglib.png and b/static/images/research/kinfraglib.png differ diff --git a/static/images/research/teachopencadd.png b/static/images/research/teachopencadd.png index d82831e..b691cc6 100644 Binary files a/static/images/research/teachopencadd.png and b/static/images/research/teachopencadd.png differ diff --git a/static/images/research/teachopencadd_topics1-10.png b/static/images/research/teachopencadd_topics1-10.png deleted file mode 100644 index 30cd720..0000000 Binary files a/static/images/research/teachopencadd_topics1-10.png and /dev/null differ diff --git a/static/images/research/teachopencadd_topics11.png b/static/images/research/teachopencadd_topics11.png deleted file mode 100644 index 9b2c49e..0000000 Binary files a/static/images/research/teachopencadd_topics11.png and /dev/null differ