Debian Med Project
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Debian Med packages for pharmaceutical research

This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research.


For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

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Debian Med Pharmacology packages

Official Debian packages with high relevance

Програма для малювання хімічних сполук
Versions of package chemtool
Debtags of package chemtool:
interfacegraphical, x11
useediting, learning
works-withimage, image:vector
Popcon: 54 users (23 upd.)*
Versions and Archs
License: DFSG free

Chemtool — 2D-редактор для малювання хімічних сполук у X11 (використовується GTK+). Він підтримує багато стилів з’єднання, більшу частину видів показу тексту, що використовуються в хімії та сплайнові/дугові/криволінійні стрілки.

Малюнки можна експортувати у формати MOL і PDB, для подальшого опису — в SVG або XFig, у вигляді малюнків PiCTeX, в растрові або Postscript файли (для деяких операцій використовується програма з XFig — transfig).

Також пакунок містить допоміжну програму, cht, для обчислення формул і (точно) молекулярної ваги намальованого елемента з файлу chemtool. Cht може викликатися прямо з Chemtool або з консолі.

Please cite: Matthias Brüstle: Chemtool - Moleküle zeichnen mit dem Pinguin. (eprint) Nachr. Chem. 49(11):1310-1313 (2001)
Screenshots of package chemtool
Planning and Analyzing Dose Finding experiments
Versions of package r-cran-dosefinding
Popcon: 16 users (18 upd.)*
Versions and Archs
License: DFSG free

The DoseFinding GNU R package provides functions for the design and analysis of dose-finding experiments (with focus on pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models (using Bayesian and non-Bayesian estimation), calculating optimal designs and an implementation of the MCPMod methodology.

Please cite: Jose C. Pinheiro, Björn Bornkamp and Frank Bretz: Design and Analysis of Dose-Finding Studies Combining Multiple Comparisons and Modeling Procedures. (PubMed) Journal of Biopharmaceutical Statistics 16(5):639-656 (2006)

Debian packages in contrib or non-free

preparation of in silico drug screening projects
Versions of package raccoon
wheezy1.0-1 (contrib)all
jessie1.0b-1 (contrib)all
sid1.0b-1 (contrib)all
stretch1.0b-2 (contrib)all
sid1.0b-2 (contrib)all
Popcon: 0 users (3 upd.)*
Versions and Archs
License: DFSG free, but needs non-free components

The field of computational biology is all about modeling physiochemical entities. Structural biology is about how those entities look in 3D and behave. Assume a specific behaviour (and only this) of a drug can be changed in a defined way.

Some good part of the characterisation of promising drug-like compounds for their interaction with a larger protein can be done on computers. This package helps with getting collections of small ligands prepared to be fitted against a particular protein of known structure. That docking itself is then to be performed by autodock or autodock-vina.

Raccoon may not find the drug, but it may well find a lead to it. To have this package with Debian shall help smaller biochemistry labs and grants an opportunity for the general public to educate itself and/or actively join in to help the world .... just a bit.

Please cite: Sandro Cosconati, Stefano Forli, Alex L Perryman, Rodney Harris, David S Goodsell and Arthur J Olson: Virtual screening with AutoDock: theory and practice. (PubMed,eprint) Expert Opinion on Drug Discovery 5(6):597–607 (2010)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 190639