Models from secondary structure and distance constraints alone?
[it appears that I accidentally sent this to the listowner rather than the list. oops. sorry Ben]
This may seem like a rather strange question, but is it possible to get Modeller to output a PDB structure based only on secondary structure information and a few distance constraints (primarily dicystene relationships). I realize that without an alignment to a known structure, anything that is generated probably bears little resemblance to reality, but I have a relatively short fragment that isn't significantly related to anything in the PDB, and between the disulfide linkages and a couple other known constraints, there aren't that many ways that it could bend together. Basically, I'm trying to generate a consistent structure that is in a possible conformation that doesn't violate steric boundaries and such, without having to manually generate the coordinates from the helix and sheet parameters. Can anyone make any suggestions?
Thanks, Andy
Andrew D. Fant wrote: > This may seem like a rather strange question, but is it possible to get > Modeller to output a PDB structure based only on secondary structure > information and a few distance constraints (primarily dicystene > relationships).
Sure, you can do that. First, you can build a model using only the primary sequence: http://salilab.org/modeller/9v2/manual/node172.html
Next, you can build whatever restraints you want, optimize, and write out the PDB file: http://salilab.org/modeller/9v2/manual/node250.html
That example builds only stereochemical restraints, but you can add the same sorts of restraints that you can add to automodel, such as distance or secondary structure restraints.
Ben Webb, Modeller Caretaker
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Andrew D. Fant -
Modeller Caretaker