Finding Secondary Structure of a Protein

[nhabibi]

Hi everybody,

I want to write a program to predict the contact mao of proteins. It uses some features as Neural Network input. One of them is Secondary structure. I know that a popular method is DSSP. I got the previously calculated dssp file for some proteins form the internet, but they don't match with their pdb files. for example you can compare the 1a1v.pdb and 1a1v.dssp, the dssp file is longer!
Another way, I think, is to use the dssp program directly, but I can't fine a free version on th internet. Can anybody help me? I really need it. glare.gif

Thanks

[nash73]

Hi nhabibi,

Could you rephrase your question once again? What do you mean by saying that "the dssp file is longer" ? I checked 1a1v.pdb and 1a1v.dssp and found nothing weird. The sequence and the secondary structure are the same. Besides, many structure-displaying free softwares with dssp algorithm embedded are on the Internet. For example, Rasmol is an easy-to-use software and you may give it a try. If you don't feel it good enough, perhaps you can directly go to dssp homepage (http://swift.cmbi.ru.nl/gv/dssp/) to download the Windows/Linux executable.

Good luck!

[auymle]

Please check the IP:http://swift.cmbi.ru.nl/gv/dssp/

DSSP is distributed on a basis of trust. You send the license agreement and you download the software. If you are a commercial entity, you mail me that you are doing this. To get DSSP proceed as follows:

1. AFTER faxing the license form to the FAX number indicated at the form (+31 (0)24 3619395) you can extract the DSSP distribution by clicking here or from the anonymous FTP area of ftp.cmbi.ru.nl. Do a cd to pub/molbio/software and download dsspcmbi.zip . In any case, type unzip dsspcmbi.zip to unpack, then look at README.TXT. If your Unix system cannot unzip, download the .tar.gz file instead.
2. Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt
3. Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code.