Pyteomics v1.0.0

[Anton Goloborodko]

Hi, dear colleagues!

We have great news for you: Pyteomics v.1.0.0 was finally released!

For those, who are not familiar with this name, Pyteomics is a Python
framework for proteomics data analysis. Its main purpose are
reproducible data analysis and rapid software prototyping. We put
special emphasis on good programming practices, testing and
documentation.

Pyteomics is hosted at the following sites:
- Python package @ Python Package Index: http://pypi.python.org/pypi/pyteomics
- project documentation @ python.org: http://packages.python.org/pyteomics
- source code @ bitbucket: http://hg.theorchromo.ru/pyteomics
- mailing list @ Google: https://groups.google.com/group/pyteomics

We would be pleased to hear your opinions and suggestions.

With best regards,
Anton & Lev.

[笹川立]

Hi, dear  Anton

I was working on prediction project for long time ago.

Recently I have known the presence of the program, and tested it on web.

The result is very poor, but still I am very interested in

your work. Because  your work is based on theoretical background.  

I have  questions concerning equations which appeared in AnalChem. 2006,78, 7770.

The first is equation for Kd(5).

How do you derive it?

To me this does't match the definition of Kd, partition coefficient.

My thinking is as follows:

According to format of Robert Rubin(J.Chemical physics 43,7,(1965)

kd (when the first monomer is at surface) should be:

  Probability at surface  = P(0,0) + P(D-1,0) + +++++++++ P(0,N) + P(D-1,N)

  Probability at in solvent = P(1,0) + + + P(1,1) + P(2,1) + P(2,2) + ++++ P(1,N) + P(2,N) ++++P(D-2,N)

 Therefore Kd   = Probability at surface  /  Probability at in solvent 

I can not derive equation 11 also.

 

I am greatly appreciated if you could answer to my questions..

With best regards,
Tatsuru Sasagawa.