Computational Tools for Cheminformatics and Biomolecular Discovery

The web apps listed here, associated APIs & CLIs, assorted tools and source code, are provided to the global scientific community free of charge, in support of open science, and to foster communication and collaboration. The Scientific Web Apps Team of the Translational Informatics Division develops software tools including web apps to support extramurally funded research projects, and strives to share methods and tools widely. If you make use of these tools and publish your research, please cite the resources appropriately.

It’s a Badapple version 2.0 with improved features. Badapple = Bioactivity datamining associative promiscuity pattern learning engine.
Badapple 2.0: An Empirical Predictor of Compound Promiscuity, Updated, Modernized, and Enhanced for Explainability, JA Ringer, CG Lambert, SB Bradfute, CG Bologa, & JJ Yang, J. Chem. Info & Modeling, 2025.
Powered by: RDKit

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Powered by: ChemAxon, Cytoscape

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Convert mol formats
Powered by: ChemAxon

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Depict molecules
Powered by: RDKit

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Distance-geometry conformer generation
Powered by: RDKit, JSmol

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Dose-response app for potency exploration: Visualize dose-response curves with 4-parameter logistic regression plots.
Powered by: R, R-dr4pl, R-Shiny
Powered by: Django, PostgreSQL, ChemAxon

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Expression profile analytics, with SABV (sex-as-biological-variable), with RNA-seq data from GTEx
Powered by: R, R-Shiny

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JavaScript molecular editor, by P. Ertl & B. Bienfait
Powered by: peter-ertl.com

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Molecule clouds (algorithm by P. Ertl & B. Rohde, Novartis)
Powered by: ChemAxon

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Lipinski Rule of 5 analysis
Powered by: ChemAxon, VCCLAB/eADMET
SMARTS filtering with built in Glaxo, Blake, and Oprea SMARTS sets
Powered by: RDKit, React, TypeScript, Vite, Docker

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TIN-X: Target importance and novelty explorer
Powered by: Python, ES6, SASS, Linting, MySQL, Solr, Docker, etc.

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TIGA: Target Illumination GWAS Analytics. From the NIH IDG Project, aggregated evidence from the NHGRI-EBI GWAS Catalog for gene-trait associations
Powered by: R, R-Shiny

Maintenance

Druglikeness using DRUGS/ACD fragment analysis
Powered by: ChemAxon

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Drug repositioning database, developed by Adam Brown and Chirag Patel at Harvard, updated by Jeremy Yang at UNM with new versions of DrugCentral, AACT, and UMLS.
Powered by: R, R-Shiny

Sincere thanks to the software developers, projects, and partners whose cooperation and commitment to open science and academic research allow these services to exist:

Allowed Use

ALLOWED USE: These applications are for limited, reasonable use by the scientific community and especially academic and non-profit researchers worldwide. Overuse will interfere with access and performance for others, so please be considerate. In general, all users should limit use to 10k molecules per day. All usage is logged, and overuse may result in client IP blocking.

Input file sizes: Note that these web apps, given typical network throughput, are impractical for large input files. In most cases the app restricts input file sizes. In general files in excess of a few thousand lines (e.g. SMILES) should not be uploaded.

Contact & Support

To report a problem with these web apps, contact Bivek Sharma Panthi.

To submit a software issue, please use the corresponding GitHub issues forum.

To inquire regarding a research collaboration, or for special requests such as high-volume jobs and collaboration inquiries contact Jeremy Yang.

Scientific Web Apps Team

  • • Jack Ringer, MS – Computer Science, Data Scientist
  • • Bivek Sharma Panthi, BS-student, Computer Science, Research Assistant
  • • Bat Ochir Artur, BS – Computer Science, Visiting Scholar
  • • Vincent T Metzger, PhD – Post-doctoral Researcher
  • • Jeremy J Yang, PhD – Research Associate Professor

Past Contributors

  • • Daniel Cannon, MS – Computer Science, Founder and President, Elevato-Iterative
  • • Jayme Holmes, MS – IT Project Manager
  • • Priyansh Kedia, MS – Visiting Scholar