Re: Software for Viewing the Effect of Amino Acid Modifications (or Substitutions) on Secondary Stru

Iddo Friedberg (
Sun, 9 Jun 1996 11:30:15 +0300 (GMT+0300)

On Sat, 8 Jun 1996, Catherine O'Malley wrote:

> Here's kind of a wild question. I wonder if anyone knows of software
> that could do the following: Suppose you had a protein with a PDB file
> entry. Naturally, you could visualize the structure using Rasmol. But
> say you wanted to find out how chemical aging of amino acid residues
> might affect secondary structure. Is there a program that would allow
> you to do this? Also, is there any software that permits you to examine
> the effect of amino acid substitutions on secondary structure? I know
> this is a longshot, but I thought I'd ask anyway.

I'm not sure how good this is. However:

One way to go about this is to use 2nary-struct prediction programs
on the web. For that you only need your sequence, not the PDB file. Submit
the original sequence first, and see if there isn't a wild deviation
between the prediction program's reply, and the actual 2ndary structure.
Those program tend to miss at the edges of a 2ary structures. That is,
they predict correctly where an alpha or beta might be, but their edges
might be wrong. Once you have this as a positive control, submit the
modified sequence.

Those programs may be reached via ExPASy.

Good Luck,



Iddo Friedberg ("\''/").___..--''"`-._ Phone: (972)-2-6585459/3 `9_ 9 ) `-. ( ).`-.__.`) email: (_Y_.)' ._ ) `._ `. ``-..-' web: _..`--'_..-_/ /--'_.' .' Random quote: You will be surprised by a loud noise.