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rna-ligand-based

Evaluation of ligand based methods applied to RNA and DNA targets

https://github.com/filipspl/rna-ligand-based

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    DOI references
    Found 5 DOI reference(s) in README
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    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary

Keywords

cheminformatics molecular-fingerprints rna virtual-screening
Last synced: 6 months ago · JSON representation

Repository

Evaluation of ligand based methods applied to RNA and DNA targets

Basic Info
  • Host: GitHub
  • Owner: filipsPL
  • License: cc-by-4.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 111 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 6
Topics
cheminformatics molecular-fingerprints rna virtual-screening
Created 9 months ago · Last pushed 8 months ago
Metadata Files
Readme License Citation Zenodo

README.md

RNA Ligand-Based Similarity Analysis

[!NOTE] This repository contains data and scripts for analyzing ligand-based similarity metrics and molecular fingerprints in the context of RNA-targeted small molecule discovery. The content is related to scientific publication

Dvid Bajusz, Anita Rcz, Janusz M. Bujnicki, and Filip Stefaniak, Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders.

DOI DOI: 10.5281/zenodo.15683151

Repository Structure

1-fingerprints/

Contains molecular fingerprint datasets in compressed CSV format. Each file represents a different fingerprinting method (e.g., CDK ECFP, FCFP, MACCS, PubChem, Indigo, MAP4, OpenBabel, RDKit, random bits).

descriptors/

Contains molecular descriptors calculated for all ligands.

3-metrics/

Contains statistical analyses and metrics, including t-tests comparing the performance of different methods and random baselines.
- metrics__ttest.csv: Summary of statistical tests for various methods. - combined_best_metrics.csv.gz: combined values for all methods and all similarity metrics - individual_metrics/: Individual metrics for fingerprints (all subdirectories) and individual ligand-based methods (tanimoto directory). The best-performing variants of all methods are in _best directory.

p-values

Contains average values for the performance metrics with the statistical significance p-values

4-ANOVA/

Contains results of ANOVA analyses and interaction means for different factors: - F1_weighted_means.csv, F2_weighted_means.csv, F3_weighted_means.csv: Weighted means for different factors. - F1_F2_interaction_means.csv, F2_F3_interaction_means.csv, F3_F1_interaction_means.csv: Interaction means between factors.

Pooled_ROC

Plots of pooled ROC curves for selected methods and all targets

5-case-study/

Contains case studies data for Glutamine_RS.

6-FP3_analysis/

Contains results of FP3 fingerprint analysis.

code/

Programs used to perform calculations.

Citation

If you use this repository or its data in your research, please cite the relevant publication or acknowledge the authors.

Owner

  • Name: filips
  • Login: filipsPL
  • Kind: user
  • Location: Warsaw, Poland
  • Company: @thervira @genesilico

- computer aided drug design + medicinal chemistry - python programming, web devel - ML - QSAR, tox prediction - :swimmer: :bicyclist: :runner:

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Issues and Pull Requests

Last synced: 7 months ago