A Polite Request...

The popularity of the Peter Kenny Generator has led to calls for a Roger Sayle Machine. The dearth of direct quotes, however, may mean it will generate sentences randomly from an approved lexicon. If you have any (documented, please) suggestions for additions, please leave them in the comments. These can be complete sentences or just phrases. Thank you.

Eat More Curry

Curcumin identified as a aminopeptidase N (APN) inhibitor.


APN also plays a significant role in angiogenesis. Angiogenesis, the formation of new blood vessels, is essential for tumor growth and the transmission of cancerous cells from the original site to new ones. Past studies have shown that curcumin can arrest angiogenesis, leading researchers to enter the chemopreventitive agent into Phase I clinical trials for cancer chemoprevention by the National Cancer Institute.

Some claim it is also good for the skin; some husbands of those making such claims assert it turns you orangey.

XML User Interface Language

Mozilla's XUL (XML User Interface Language) - which, I am informed, rhymes with cool - is proving useful for formatting GUIs. Nice tutorials are here.

Method for Computing Protein Binding Affinity

Via arXiv, using a Monte Carlo method to compute the binding affinity of a ligand to a protein [pdf]


The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.

Shiny Disk Make Rainbow

A list of links to tutorials on various aspects of using RasMol and Chime. Also, a list of animations of proteins created using Ribbons and RasMol.

Java CML Filter Library

The Java CML filter library, found via Openscience.org


The library makes use of the Chemical Data Object Programming Interface (CDOPI). Using the JCF Library means that the Java program must define a class that implements CDOPI. JCFL uses this subclass to store information taken from a CML file or stores the information in the subclass into a CML file.

Supports JMol animationN, JChemPaint, PDB and MDLMol files.

Peter Kenny in Electronic Form

If there's not enough Peter Kenny in your life, please direct yourself to the Jargosaurus-approved Random Peter Kenny Generator. Way-Hey!

SMILES Depicters

Various SMILES depicters on the Web, including:


JME Molecular Editor

Daylight Depict

JMDraw/SmilesViewer applet

SMi Drug Design Conference

SMI Group's Drug Design conference, The Hatton, London, 23-24 February. Followed by the High Throughput Molecular Docking symposium on the 25th.


The primary purpose of this interactive workshop is the identification and discussion of the critical issues related to using high-throughput molecular docking (HTMD) as a source for novel lead molecules. Delegates will receive an overview of different algorithms and processes for effectively carrying out HTMD and gain a better understanding of opportunities and limitations, ligand-related issues, target processing, docking schemes and scoring functions, measuring performance and emerging technologies.

It'll be interesting to see who chooses to go to this instead of MUG.

A Robot Scientist

Machine built to mix and examine knockout yeast cultures.


Though they chose genetics to test their idea, Dr King and his colleagues think it could be applied to other fields where vast numbers of small, fiddly experiments need to be done in order to arrive at a result—for example, drug design and certain sorts of advanced chemical synthesis. One question is, if their robot does make an important discovery, will it be eligible to win a Nobel prize?

Funny, most of the scientists I know are such animated people. I can't imagine this one fitting in at all.

Petty Criminals and Tableware

Join the MUGgers and CUPpers at the 2004 Daylight and OpenEye conferences in Santa Fe, conveniently scheduled one after the other.


Drugs are good (Good drugs are better). Pat Walters, Vertex Pharmaceuticals

Talking to Chemists: When louder isn't enough. Roger Sayle

Astex Viewer

We've been looking at proteins in Astex Viewer.


It can be used as an Applet in a web page and as a desktop application. The software should run on most operating systems and in most internet browsers ... The Electron Density page shows reconstructed electron density for protein/ligand complexes from the extended GOLD validation set. This validation set was selected by Astex and the Cambridge Crystallographic Data Centre. The electron density has been generated for the 70 complexes for which structure factors have been deposited at the Protein Data Bank.

Note careful use of the word 'most.' Still, pretty neat.

About this site
COSMAS is a weblog dedicated to topics of interest in informatics, particularly (but not limited to) chemoinformatics. If you see an article or tool of interest to you, please let us know.
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January 2004
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November 2003
Recent Entries
A Polite Request...
Eat More Curry
XML User Interface Language
Method for Computing Protein Binding Affinity
Shiny Disk Make Rainbow
Java CML Filter Library
Peter Kenny in Electronic Form
SMILES Depicters
SMi Drug Design Conference
A Robot Scientist
Petty Criminals and Tableware
Astex Viewer
"Other" Bioinformatics
Calculating Molecular Descriptors
Creating your first ontology
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