Orhan Karsligil's Ideas, Thoughts and Collection of Resources

Multidimensional signatures in antimicrobial peptides


Author: Nannette Y. Yount, Michael R. Yeaman

Year: 2005

Category: Bioinformatics Peptides Antimicrobial

Publisher: PNAS

DOI: 10.1073

My short notes

3D motif discovery for antimicrobial peptides: multidimensional signature model. This is a unifying structural theme. Has evolutionary roots, predicts not yet existing peptides and identified known peptides to have antimicrobial properties.

Common peptide properties (i) small proteins (<10kDa), (ii) cationic charges (+2/+7 at pH7), (iii) amphipathic (hydrophobic and hydrophilic facets).

Select a set of peptides from a known set, also include known peptides with yet unknown antimicrobial property but structural similarities.

Prepare a protocal to test the antimicrobial effects (assay for antimicrobial activity).

My ideas

  • Embedding Antimicrobial Peptides on the surfaces.

  • Coctail of peptides to check if their interaction with the organisms are based on different processes

Tags: Bioinformatics 3D Motifs Signatures

Structured Blogging

When I started blogging I wanted to be organized. I wanted to keep the information I find from different sources in a well thought manner. Well... that does not happen easily. There are too many categories things belong to, too many "one-to-many", "many-to-many" relationships. It also does not help that one day you type longer and make a good description and the other day you get lazy and only put a link, which does not make any sense 2 weeks later.
So I started looking around for a framework that would force me to be more structured. Ultimately I am planning to use this blog to keep a diary of my research. And when you do research you think of many different subjects all floating around without any solid ties to anything, but you have some idea how they might relate to other things. Writing down a sentence does not capture that soft relationship. One needs to be forced to write down all the details, so that it can be used later.
Finally 2 days ago I found something that might work: Structured Blogging plugin for Wordpress. From now on I am planning to move onto the templates for structured blogging plugin. They provide a template and force you to fill in required information. When you edit, the underlying data is well structured. The diary format turns into a database format, that can be maintained. Dividing the usefull information into bins helps a lot. When displayed it looks like a single coherent post but in the background it is a collection of sub data structures.
I will try to use it as much as possible in the future. I will post an update how things go.

Technorati Tags:

The articles I read and plan to read

I mentioned CiteUlike before. I use it to store articles that I read or plan to read. It keeps all the relevant referencing information, links to the journals and even to the PDF if you uploaded one. This way I can access the papers I am interested in from anywhere. It is also nice to be able to search for papers by title, author, abstract etc. Sometimes you find papers by looking at other people's libraries. If they share same tastes as you do the chance that they have interesting articles is also high.

You can reach my library from this link: Orhan's library

Guy Kawasaki's Blog

Guy Kawasaki

Job: VC (founder), at

Blog: “Let the Good Times Roll” by Guy Kawasaki


More about history of Guy Kawasaki can be found at his blog:

History and Story of Guy Kawasaki

Deal Finder Search Engine

If you are looking for cool deals on internet there are couple site people visit regularly. Apex is one I believe, also mwave and newegg are good places to start with. But this site is the best. It is a deal search engine. It comes up with multiple results for the things you are searching for, complete with coupon and rebate information. Very useful site.
Find great deals from the best websites on the newest products