[Biojava-l] GSoC project question

[Jianjiong Gao]

Hello,

My name is Jianjiong Gao, a graduate student in Computer Science
Department at University of Missouri-Columbia. I am very interested in
applying for your GSoC project "Identification and Classification of
Posttranslational Modification of Proteins". This project is highly
related to my dissertation topic "Bioinformatic analysis and
prediction of phosphorylation and other PTMs." Although I have not
touched the structural part of PTM till now, I am really interested in
learning and expanding my research on this field.

After reading the project description on the idea page
(http://biojava.org/wiki/Google_Summer_of_Code), I have several
questions regarding the *approach* section:

> 1. Establish a list of known PTMs and write code to locate these PTMs in a 3D protein structure.

Q1: There are many different types of PTMs. Do you have list of PTMs
of interest? Do you have priorities on different PTMs?
Q2: Is there any available algorithm to locate the PTMs in a 3D
protein structure? What is the difficulty on this task?
Q3: The PDB file contains annotations of residue modifications such as
HETATM AND MODRES. Can we utilized this information for localizing the
PTMs?

> 2. Determine the protein residues that carry PTMs based on distance thresholds.
> 3. Traverse the sugar molecules and establish their link pattern based on connectivity.

Q4: Is this task to determine the types of glycosylation, i.e.,
N-linked glycosylation, O-N-acetylgalactosamine, O-glucose, etc?
Q5: Is there any available algorithm to do this? What is the
difficulty in this task? It looks complicated with so many different
types of glycosylation and structure isomers.

> 4. Present the PTMs as text in a linear notation and 2D graphical representations if time permits.

Q6: Can we used the SMILES format
(http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification)
here? Or do we have any other better options?

Thanks very much for your time. I am looking forward to hearing from you.

Best Regards,
-JJ