Custom protein sequence

Started by vladimirgainullin

palardyg Lv 1

I was hoping to do the same thing. I did not get any response on importing my own PDB files or sequence. I have been using Deepview for modeling. It seems to be the only freeware out there. http://spdbv.vital-it.ch/index.html. Still can't get it to ligate my individual domains together after merging my layers.

axcho Lv 1

It's within the realm of possibility, but it's unlikely to be a support feature any time soon.

The main reason is that we still need to prove that humans can be more effective than computers at this whole protein-folding thing. And if we make it easy for players to look at existing computer-generated proteins, our evidence becomes less trustworthy in the eyes of some critics.

DMahalko Lv 1

It seems like one of the better ways to learn how to do this is to look at how real proteins are modeled. I do not see how explicitly choosing to prevent people from learning how proteins should be built is going to help improve the process.

So, as an uneducated non-molecular-biologist, am I "cheating" if I go to the Molecule of the Month website, download a protein PDB, and look at it with a viewer like Avogadro or Chimera?

RCSB Protein Data Bank / Molecule of the Month
http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html

Avogadro viewer:
http://avogadro.openmolecules.net/

UCSF Chimera viewer:
http://www.cgl.ucsf.edu/chimera/

I was contemplating adding basic info on how to view real PDBs to the wiki, but seeing this thread I am not sure if I should do that.

axcho Lv 1

Looking at proteins in general is fine. In fact, it's probably a good idea.

The problem is if people look at the actual protein, for an existing science puzzle. Then you'd have the answer right in front of you. Some of the science puzzles are for known proteins.

DMahalko Lv 1

I am going to take your response as a tentative suggestion that a page on finding, downloading, and viewing PDBs is acceptable on the wiki, and so I have started one:

http://foldit.wikia.com/wiki/Viewing_real_protein_models

I am NOT an expert so this is probably going to need help from the real scientists and modelers. Also it is a work in progress and at an early development stage right now.

If you don't want this, I will try to find another home for a page like this. (backup copies saved)

biassoni Lv 1

HEGFRRKPSLLAHPGPLVKSEETVILQCWSDVMFEHFLLHREGTFNHTLRLIGEHIDG
VSKGNFSIGRMTQDLAGTYRCYGSVTHSPYQLSAPSDPLDIVITGLYEKPSLSAQPGP
TVLAGESVTLSCSSRSSYDMYHLSREGEAHERRLPAGTKVNGTFQADFPLDPATHG
GTYRCFGSFRDSPYEWSKSSDPLLVSVTGNSSNSWPSPTEPSSETGNPRHLH