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Update 2023 #58

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Apr 9, 2024
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9a55107
DRAFT update environemnt
kabu00002 Sep 7, 2023
4a890fc
WIP: updated README and env, and fixed bug
kabu00002 Sep 8, 2023
684dd2c
fixed bugs
kabu00002 Sep 8, 2023
1fafa84
change rkdit version
kabu00002 Sep 15, 2023
bce4407
add new fragemnt library and updated pandas
kabu00002 Sep 28, 2023
653e11f
Workaround that images appear in DF in some cases
kabu00002 Sep 28, 2023
1879718
updated notebooks 2_
kabu00002 Sep 28, 2023
a4d3dc9
fixed rdkit version mess
kabu00002 Sep 28, 2023
b32b4b8
fragment lib reduction
kabu00002 Sep 28, 2023
72fa6b7
Updated notebooks (excluding 4)
kabu00002 Sep 28, 2023
31721c8
added citation
kabu00002 Nov 15, 2023
bc1b219
add link to citation
kabu00002 Nov 15, 2023
59548a5
added list of publications
kabu00002 Nov 15, 2023
b9c0180
WIP
kabu00002 Dec 12, 2023
867c5dd
added new fragment library
kabu00002 Dec 12, 2023
6cffce9
re-run notbooks
kabu00002 Dec 12, 2023
e4b763a
fragment-library reduced and filtered on modified fragment library
kabu00002 Dec 12, 2023
851ce40
solved review notebooks
kabu00002 Jan 24, 2024
cbbb2a5
resolve review
kabu00002 Jan 24, 2024
ebfd127
list of pupblications: suggestions
kabu00002 Jan 24, 2024
0c5af7e
rerun notebooks 4.1-4.3 and 4.5
kabu00002 Jan 31, 2024
47b29ac
lis of publ.
kabu00002 Jan 31, 2024
6546fd9
fixed chembl API problem
kabu00002 Feb 7, 2024
fcc80c4
added Paper
kabu00002 Feb 14, 2024
a467e35
Removed inkscale stuff
kabu00002 Feb 14, 2024
b7fbefa
added all pubs
kabu00002 Feb 14, 2024
17b037c
number of atoms delted
kabu00002 Feb 14, 2024
f6d109a
Merge branch 'dev' into update_2023
PaulaKramer Feb 19, 2024
530dd31
added Paper to list of publications
kabu00002 Mar 20, 2024
2715a60
updated mail
kabu00002 Mar 20, 2024
8ddb795
ci build conda env fails
PaulaKramer Feb 15, 2024
ca572fa
changed python version env, removed ci py3.10
PaulaKramer Feb 16, 2024
7920196
update actions checkout
PaulaKramer Feb 16, 2024
8b92b6d
update setupminiconda version
PaulaKramer Feb 16, 2024
bb12621
include python 3.9
PaulaKramer Feb 16, 2024
e4e2e41
changed pip install of kinfraglib
PaulaKramer Feb 16, 2024
3ca80c7
ci remove py3.11, add mac py3.9
PaulaKramer Feb 16, 2024
38f29b9
add windows to ci
PaulaKramer Feb 19, 2024
4b8263c
small ci changes
PaulaKramer Feb 19, 2024
65bd255
increased timeout ci
PaulaKramer Mar 22, 2024
1c001d6
changed zenodo doi in ci
PaulaKramer Mar 22, 2024
ee3139a
remove ci warning, reduce timeout
PaulaKramer Mar 22, 2024
76fccc7
test remove mac from ci
PaulaKramer Mar 22, 2024
f35eef7
timeout ci
PaulaKramer Mar 22, 2024
4e27f29
Merge pull request #62 from volkamerlab/ci_testing
PaulaKramer Mar 25, 2024
bb4a272
updated zenodo doi in combinatorial readme
PaulaKramer Mar 26, 2024
4663e19
updated notebooks readme
PaulaKramer Mar 26, 2024
ffc0cdf
added klifs version to readmes
PaulaKramer Mar 28, 2024
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12 changes: 12 additions & 0 deletions CITATION.bib
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
@article{doi:10.1021/acs.jcim.0c00839,
author = {Sydow, Dominique and Schmiel, Paula and Mortier, Jérémie and Volkamer, Andrea},
title = {KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination},
journal = {Journal of Chemical Information and Modeling},
volume = {60},
number = {12},
pages = {6081-6094},
year = {2020},
doi = {10.1021/acs.jcim.0c00839},
note ={PMID: 33155465},
URL = {https://doi.org/10.1021/acs.jcim.0c00839}
}
9 changes: 7 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,12 @@ fragments in order to generate novel potential inhibitors.
# Change to KinFragLib directory
cd /path/to/KinFragLib

# Create and activate environment
# Create environment
conda env create -f environment.yml
# When using a MacBook with an M1 chip you may need instead:
CONDA_SUBDIR=osx-64 conda env create -f environment.yml

# Activate environment
conda activate kinfraglib

# Install the kinfraglib pip package
Expand Down Expand Up @@ -95,7 +99,7 @@ This resource is licensed under the [MIT](https://opensource.org/licenses/MIT) l

## Citation

Sydow, D., Schmiel, P., Mortier, J., and Volkamer, A. KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. J. Chem. Inf. Model. 2020. https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00839
[Sydow, D., Schmiel, P., Mortier, J., and Volkamer, A. KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. J. Chem. Inf. Model. 2020. https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00839](CITATION.bib)

```bib
@article{doi:10.1021/acs.jcim.0c00839,
Expand All @@ -111,3 +115,4 @@ note ={PMID: 33155465},
URL = {https://doi.org/10.1021/acs.jcim.0c00839}
}
```
## List of publications
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