[Biopython] About Google Summer Code Project PDB-tidy

[Diana Jaunzeikare]

Hi Fuxiao,

Good start on the application! Some comments below.

On Wed, Apr 7, 2010 at 9:40 PM, Fuxiao Xin <fuxin at umail.iu.edu> wrote:
> Dear all,
>
> I am a third year Phd student in Bioinformatics from Indiana University
> Bloomington.  I am very in interested in the google summer code project of
> biopython "PDB-Tidy: command-line tools for manipulating PDB files".
>
> My own research needs extensive manipulation of PDB files, and I think  this
> idea of adding more features to Bio.PDB and more command line options to
> analyze/present PDB data is excellent. This project is of strong interest to
> me since it will benefit my own research project as well.
>
> Programming Skills: I use perl and python during my daily research. I am now
> working on developing a new functional site predictor using protein
> structure information. The code will be open source, but the work is under
> review so the code is not released yet.
>
> My project plan:
>
> week1
> 1. Renumber residues starting from 1 (or N)
> function name: renumberPDB, given a pdb file, rename the atom field
> numbering of the file to remove missing amino acids
> communicate with mentors to set standards of the code to follow for the rest
> of the functions
> create work log to keep track of process;
>
> week2-3
> 2. Select a portion of the structure -- models, chains, etc. -- and write it
> to a new file (PDB, FASTA, and other formats)
> function name: rewritePDB, inputs will be a particular portion of a PDB file
> you want to write out(support 'chain', 'model', 'atom'), a file format(PDB,
> fasta), and the output name.
> 3. Perform some basic, well-established measures of model quality/validity
> function name: PDBquality
> the function will report RESOLUTION and ? of the structure

Maybe you can get some inspiration of measures of model
quality/validity from PDBREPORT database [0] and WHAT_IF [1] software.

[0] http://swift.cmbi.ru.nl/gv/pdbreport/
[1] http://swift.cmbi.ru.nl/whatif/


> 4. extract disorder region in PDB structure
> function name: PDBdisorder
> report missing residues in the structure atom field
>
> week3-4
> 5. make a function to draw a Ramachandran plot
> function name: ramaPLOT
> combine the two steps(calcualting torsion angles and draw the plot) into one
> function, give the option to draw the plot or not
>
> week5
> 6. open PDB files in the window for visulization, visulize PDBsuperpose
> results, output RMSD
> function name: superposePDB
> the function will look like the PDBsuperpose function in matlab; use
> Bio.PDB.Superimposer() to perform the superimpose, use Jmol or other
> visulization tool to see the results
> week6
> 7. write a function to extract all experimental conditions of a PDB file,
> includes PH, temperature, and salt
> function name: PDBconditon
> it will be easy to get PH and temperature information, but for salt, it will
> be hard to parse because there is no general rule of such information in the
> PDB file; parse REMARK 200 field;
>
> week7-8
> 8. extract PTM,
> function name: PDBptm
> difficult: the Post-translational modification annotation in PDB is not
> consistant, need to make a list of PTMs to work on
> parse MODRES field
>
> week9-10
> 9. extract ligand binding information
> function name: PDBligand
> parse HETNAM field
>
>
> Other obligations:  I am aware that google summer code starts from May 24th,
> but I will have a review paper with my advisor due on June 1st, I hope it
> will be OK for me to start after June 1st, and I will makeup the first week
> in Auguest.
>
> Best,
> Fuxiao
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