Skip to content

Commit

Permalink
add entries
Browse files Browse the repository at this point in the history
  • Loading branch information
Tonylac77 committed Jan 8, 2025
1 parent e321ec5 commit 4092386
Show file tree
Hide file tree
Showing 160 changed files with 2,886 additions and 1,328 deletions.
6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,9 @@ The [CADD Vault](https://drugbud-suite.github.io/CADD_Vault/) includes resources
- Machine Learning Applications in Drug Design
- Fragment-Based Drug Design (FBDD)
- Datasets for Drug Design
Number of publications: 1128
Number of code repositories: 957
Number of webserver links: 150
Number of publications: 1146
Number of code repositories: 969
Number of webserver links: 161
Number of webserver links: 123


Expand Down
Binary file modified cadd_vault_data.xlsx
Binary file not shown.
34 changes: 24 additions & 10 deletions docs/ADMET/Pretrained Models.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ icon: material/needle

## **BBB**
- **BBB-score**: The Blood–Brain Barrier (BBB) Score
[![Code](https://img.shields.io/github/stars/gkxiao/BBB-score?style=for-the-badge&logo=github)](https://github.com/gkxiao/BBB-score) [![Last Commit](https://img.shields.io/github/last-commit/gkxiao/BBB-score?style=for-the-badge&logo=github)](https://github.com/gkxiao/BBB-score) [![Publication](https://img.shields.io/badge/Publication-Citations:203-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jmedchem.9b01220)
[![Code](https://img.shields.io/github/stars/gkxiao/BBB-score?style=for-the-badge&logo=github)](https://github.com/gkxiao/BBB-score) [![Last Commit](https://img.shields.io/github/last-commit/gkxiao/BBB-score?style=for-the-badge&logo=github)](https://github.com/gkxiao/BBB-score) [![Publication](https://img.shields.io/badge/Publication-Citations:204-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jmedchem.9b01220)

## **CYP450**
- **D-CyPre**: Tool for Accurately Predicting the Site of Metabolism of Human Cytochrome P450 Metabolism
Expand All @@ -15,47 +15,61 @@ icon: material/needle

## **General**
- **ADMET_XGBoost**: ADMETboost: a web server for accurate ADMET prediction
[![Code](https://img.shields.io/github/stars/smu-tao-group/ADMET_XGBoost?style=for-the-badge&logo=github)](https://github.com/smu-tao-group/ADMET_XGBoost) [![Last Commit](https://img.shields.io/github/last-commit/smu-tao-group/ADMET_XGBoost?style=for-the-badge&logo=github)](https://github.com/smu-tao-group/ADMET_XGBoost) [![Publication](https://img.shields.io/badge/Publication-Citations:37-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1007/s00894-022-05373-8)
[![Code](https://img.shields.io/github/stars/smu-tao-group/ADMET_XGBoost?style=for-the-badge&logo=github)](https://github.com/smu-tao-group/ADMET_XGBoost) [![Last Commit](https://img.shields.io/github/last-commit/smu-tao-group/ADMET_XGBoost?style=for-the-badge&logo=github)](https://github.com/smu-tao-group/ADMET_XGBoost) [![Publication](https://img.shields.io/badge/Publication-Citations:38-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1007/s00894-022-05373-8)
- **admet-ai**: ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries
[![Code](https://img.shields.io/github/stars/swansonk14/admet_ai?style=for-the-badge&logo=github)](https://github.com/swansonk14/admet_ai) [![Last Commit](https://img.shields.io/github/last-commit/swansonk14/admet_ai?style=for-the-badge&logo=github)](https://github.com/swansonk14/admet_ai) [![Publication](https://img.shields.io/badge/Publication-Citations:16-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/bioinformatics/btae416)
- **ADMETlab**:
- **ADMETlab**: systematical evaluation of ADMET properties, as well as some physicochemical properties and medicinal chemistry friendliness
[![Code](https://img.shields.io/github/stars/ifyoungnet/ADMETlab?style=for-the-badge&logo=github)](https://github.com/ifyoungnet/ADMETlab) [![Last Commit](https://img.shields.io/github/last-commit/ifyoungnet/ADMETlab?style=for-the-badge&logo=github)](https://github.com/ifyoungnet/ADMETlab) [![Publication](https://img.shields.io/badge/Publication-Citations:75-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkae236)
- **ADMETlab3.0**:
[![Publication](https://img.shields.io/badge/Publication-Citations:75-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkae236) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://admetlab3.scbdd.com)
- **ADMETlab3.0**: systematical evaluation of ADMET properties, as well as some physicochemical properties and medicinal chemistry friendliness
[![Publication](https://img.shields.io/badge/Publication-Citations:75-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkae236) [![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://admetlab3.scbdd.com)
- **ChemMORT**: ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization
[![Code](https://img.shields.io/github/stars/leelasd/ChemMORT?style=for-the-badge&logo=github)](https://github.com/leelasd/ChemMORT) [![Last Commit](https://img.shields.io/github/last-commit/leelasd/ChemMORT?style=for-the-badge&logo=github)](https://github.com/leelasd/ChemMORT) [![Publication](https://img.shields.io/badge/Publication-Citations:3-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/bib/bbae008)
- **Computation-ADME**:
[![Code](https://img.shields.io/github/stars/molecularinformatics/Computational-ADME?style=for-the-badge&logo=github)](https://github.com/molecularinformatics/Computational-ADME) [![Last Commit](https://img.shields.io/github/last-commit/molecularinformatics/Computational-ADME?style=for-the-badge&logo=github)](https://github.com/molecularinformatics/Computational-ADME) [![Publication](https://img.shields.io/badge/Publication-Citations:21-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.3c00160)
- **Datagrok Admetica**: Datagrok pretrained ADME models
[![Code](https://img.shields.io/github/stars/datagrok-ai/admetica?style=for-the-badge&logo=github)](https://github.com/datagrok-ai/admetica) [![Last Commit](https://img.shields.io/github/last-commit/datagrok-ai/admetica?style=for-the-badge&logo=github)](https://github.com/datagrok-ai/admetica) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://public.datagrok.ai/browse/admetica.admeticaapp)
[![Code](https://img.shields.io/github/stars/datagrok-ai/admetica?style=for-the-badge&logo=github)](https://github.com/datagrok-ai/admetica) [![Last Commit](https://img.shields.io/github/last-commit/datagrok-ai/admetica?style=for-the-badge&logo=github)](https://github.com/datagrok-ai/admetica) [![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://public.datagrok.ai/browse/admetica.admeticaapp)
- **QIP**: Machine learning model that predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of molecules.
[![Code](https://img.shields.io/github/stars/standigm/qip?style=for-the-badge&logo=github)](https://github.com/standigm/qip) [![Last Commit](https://img.shields.io/github/last-commit/standigm/qip?style=for-the-badge&logo=github)](https://github.com/standigm/qip) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.4c00772)
- **OPERA**:
[![Code](https://img.shields.io/github/stars/NIEHS/OPERA?style=for-the-badge&logo=github)](https://github.com/NIEHS/OPERA) [![Last Commit](https://img.shields.io/github/last-commit/NIEHS/OPERA?style=for-the-badge&logo=github)](https://github.com/NIEHS/OPERA) [![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://ntp.niehs.nih.gov/whatwestudy/niceatm/comptox/ct-opera/opera.html)
- **VEGA**:
[![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://www.vegahub.eu/portfolio-item/vega-qsar/)
- **SwissADME**: web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness
[![Publication](https://img.shields.io/badge/Publication-Citations:N/A-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1038/srep42717) [![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](http://www.swissadme.ch/)
- **OCHEM**:
[![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://ochem.eu/home/show.do)
- **vNN-ADMET**:
[![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://vnnadmet.bhsai.org/vnnadmet/login.xhtml)

## **Metabolites**
- **MetaPredictor**: in silico prediction of drug metabolites based on deep language models
[![Code](https://img.shields.io/github/stars/zhukeyun/Meta-Predictor?style=for-the-badge&logo=github)](https://github.com/zhukeyun/Meta-Predictor) [![Last Commit](https://img.shields.io/github/last-commit/zhukeyun/Meta-Predictor?style=for-the-badge&logo=github)](https://github.com/zhukeyun/Meta-Predictor) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/bib/bbae374)

## **PK**
- **Deep-PK**: deep learning for small molecule pharmacokinetic and toxicity prediction
[![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://biosig.lab.uq.edu.au/deeppk/)
- **pkCSM**:
[![Publication](https://img.shields.io/badge/Publication-Citations:N/A-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jmedchem.5b00104) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://biosig.lab.uq.edu.au/pkcsm/)
- **PKSmart**: This work used molecular structural fingerprints, physicochemical properties, and predicted animal PK data as features to model the human PK parameters VDss, CL, t½, fu and MRT for 1,283 unique compounds and developed a webhosted application **[PKSmart](https://pk-predictor.serve.scilifelab.se/)**, the first work that publicly releases PK models on par with industry-standard models.
[![Code](https://img.shields.io/github/stars/srijitseal/PKSmart?style=for-the-badge&logo=github)](https://github.com/srijitseal/PKSmart) [![Last Commit](https://img.shields.io/github/last-commit/srijitseal/PKSmart?style=for-the-badge&logo=github)](https://github.com/srijitseal/PKSmart) [![Publication](https://img.shields.io/badge/Publication-Citations:7-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1101/2024.02.02.578658)

## **Toxicity**
- **ProTox3**: Webserver for toxicity prediction
[![Publication](https://img.shields.io/badge/Publication-Citations:97-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkae303) [![Webserver](https://img.shields.io/badge/Webserver-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://tox.charite.de/protox3/)
[![Publication](https://img.shields.io/badge/Publication-Citations:106-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkae303) [![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://tox.charite.de/protox3/)
### **Toxicity**
- **Cyto-Safe**: Webserver for toxicity prediction
[![Code](https://img.shields.io/github/stars/LabMolUFG/cytosafe?style=for-the-badge&logo=github)](https://github.com/LabMolUFG/cytosafe) [![Last Commit](https://img.shields.io/github/last-commit/LabMolUFG/cytosafe?style=for-the-badge&logo=github)](https://github.com/LabMolUFG/cytosafe) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.4c01811) [![Webserver](https://img.shields.io/badge/Webserver-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](http://insightai.labmol.com.br/)
[![Code](https://img.shields.io/github/stars/LabMolUFG/cytosafe?style=for-the-badge&logo=github)](https://github.com/LabMolUFG/cytosafe) [![Last Commit](https://img.shields.io/github/last-commit/LabMolUFG/cytosafe?style=for-the-badge&logo=github)](https://github.com/LabMolUFG/cytosafe) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.4c01811) [![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](http://insightai.labmol.com.br/)

## **hERG**
- **CardioTox**: A robust predictor for hERG channel blockade via deep learning meta ensembling approaches
[![Code](https://img.shields.io/github/stars/Abdulk084/CardioTox?style=for-the-badge&logo=github)](https://github.com/Abdulk084/CardioTox) [![Last Commit](https://img.shields.io/github/last-commit/Abdulk084/CardioTox?style=for-the-badge&logo=github)](https://github.com/Abdulk084/CardioTox) [![Publication](https://img.shields.io/badge/Publication-Citations:30-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1186/s13321-021-00541-z)
- **CLOP-hERG**: Contrastive Learning Optimized Pretrained Model for Representation Learning in Predicting Drug-Induced hERG Channel Blockers
[![Code](https://img.shields.io/github/stars/heshida01/CLOP-hERG?style=for-the-badge&logo=github)](https://github.com/heshida01/CLOP-hERG/blob/main/README.md) [![Last Commit](https://img.shields.io/github/last-commit/heshida01/CLOP-hERG?style=for-the-badge&logo=github)](https://github.com/heshida01/CLOP-hERG/blob/main/README.md) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.47852/bonviewMEDIN42022049)
- **hERGdb**: web-based cardiotoxicity prediction
[![Publication](https://img.shields.io/badge/Publication-Citations:46-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1371/journal.pone.0199348) [![Webserver](https://img.shields.io/badge/Webserver-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://drugdesign.riken.jp/hERGdb/)
[![Publication](https://img.shields.io/badge/Publication-Citations:46-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1371/journal.pone.0199348) [![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://drugdesign.riken.jp/hERGdb/)

## **logP**
- **OWPCP**: OWPCP: A Deep Learning Model to Predict Octanol-Water Partition Coefficient
[![Code](https://img.shields.io/github/stars/jmohammadmaleki/OWPCP?style=for-the-badge&logo=github)](https://github.com/jmohammadmaleki/OWPCP.git) [![Last Commit](https://img.shields.io/github/last-commit/jmohammadmaleki/OWPCP?style=for-the-badge&logo=github)](https://github.com/jmohammadmaleki/OWPCP.git) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.48550/arXiv.2410.18118)
- **rescoss_logp_ml**: A repository dedicated to logP prediction using machine learning, offering insights into the solubility and distribution properties of compounds.
[![Code](https://img.shields.io/github/stars/cisert/rescoss_logp_ml?style=for-the-badge&logo=github)](https://github.com/cisert/rescoss_logp_ml) [![Last Commit](https://img.shields.io/github/last-commit/cisert/rescoss_logp_ml?style=for-the-badge&logo=github)](https://github.com/cisert/rescoss_logp_ml) [![Publication](https://img.shields.io/badge/Publication-Citations:25-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acsomega.2c05607)
[![Code](https://img.shields.io/github/stars/cisert/rescoss_logp_ml?style=for-the-badge&logo=github)](https://github.com/cisert/rescoss_logp_ml) [![Last Commit](https://img.shields.io/github/last-commit/cisert/rescoss_logp_ml?style=for-the-badge&logo=github)](https://github.com/cisert/rescoss_logp_ml) [![Publication](https://img.shields.io/badge/Publication-Citations:26-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acsomega.2c05607)
2 changes: 1 addition & 1 deletion docs/Bioinformatics/Sequence Family Classification.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ icon: material/crowd
---

- **InterPro**: resource for the classification of protein sequences into families
[![Publication](https://img.shields.io/badge/Publication-Citations:6-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar%2Fgkae1082) [![Webserver](https://img.shields.io/badge/Webserver-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://www.ebi.ac.uk/interpro)
[![Publication](https://img.shields.io/badge/Publication-Citations:6-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar%2Fgkae1082) [![Webserver](https://img.shields.io/badge/Webserver-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://www.ebi.ac.uk/interpro)
12 changes: 12 additions & 0 deletions docs/CADD Challenges/CADD Challenges.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
---
icon: material/podium-gold
---

- **CACHE**: Critical Assessment of Computational Hit-Finding Experiments
[![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://cache-challenge.org/)
- **CASF**: Comparative Assessment of Scoring Functions
[![Publication](https://img.shields.io/badge/Publication-Citations:458-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.8b00545)
- **CASP**: Critical Assessment of protein Structure Prediction
[![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://predictioncenter.org/)
- **MAINFRAME**: Global Open Science Machine Learning Network for Drug Discovery
[![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://aircheck.ai/mainframe)
2 changes: 1 addition & 1 deletion docs/Chemical Space/Chemical Space Comparison.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ icon: material/select-compare
---

- **SpaceCompare**: Comparison of Combinatorial Fragment Spaces
[![Publication](https://img.shields.io/badge/Publication-Citations:25-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.1c01378) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://www.zbh.uni-hamburg.de/en/forschung/amd/software/spacecompare.html)
[![Publication](https://img.shields.io/badge/Publication-Citations:25-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.1c01378) [![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://www.zbh.uni-hamburg.de/en/forschung/amd/software/spacecompare.html)
Loading

0 comments on commit 4092386

Please sign in to comment.