Welcome to STB ProteinArt’s documentation!

The biggest challange for a biologist or an experimentalist in computational biology field is the lack of “computational” knowledge. There are many tools out there, yet there are many times you need to write your own script. The scripts collected in this github repo are the product of those needs. They were written specifically for pentameric ligand-gated ion channels. With some modification they are applicable to any membrane protein. The future releases will cover this issue.

You will realise quickly, I do not have the programmer’s discipline. The scripts here have no proper comments or markups. Well, most of the old scripts anyways. But as you will see with PDBParser I have improved, since 2015, the first year I have created this website. If you are a newby in computational biology, I hope you will find these scripts inspirational and realise that this field is fun and not scary at all. Afterall I am a person who did not touch a computer before 2004.

My proper introduction to the terminal was not until 2009. 2010 is when I have met with python, at David Van der Spoel’s lab, as a master student. I was working together with Erik Marklund, testing a code he was developing. From there I went on to do a PhD with Erik Lindahl and Berk Hess; I have studied the dynamics of ion channels (I am in love with channels). This is also where I have started the PDBParser project, thanks to Laura Orellana. She gave me an oppurtunity to work with her and I hope to do my best. Now I am working with Alex MacKerell as a Post-Doc, learning parameterization (that’s how we spell it, I don’t know why) among other projects. You see it hasn’t even been a decade since I started, I have a lot to catch up but it is doable. You can make the change and learn how to use the terminal or programming as long as you have the interest, and you are working in a supportive environment. I cannot stress this enough. All this was possible because I have been working with people that gave me the freedom, and showed me the patience.

Maintaining this repo will help me obtain better practices. Opening the doors to my secret codes, I force myself to think from the users perspectives and improve my work. Some of these scripts are based on Samuel Murails work (like setting up GLIC simulations), some are written entirely by me. You can reach the scripts from my github page

So enjoy the site. Suggestions are welcomed (contact: ozgeyoluk_at_proteinart.net).