Sent to CCL by: Michael A Wilson [Michael.A.Wilson*nasa.gov]Regarding (a): the PLOP program from Matt Jacobson's group at UCSF, which can be used to predict and optimize loop structure ( http://http-:-//www.jacobsonlab.org ). I'm sure there are other codes to do constrained structure prediction. Regarding (b): most MD codes will allow you to constrain (either rigidly or with harmonic restraints) selected atoms, so it would be straightforward to do something like restrain all backbone atoms, except in the region of interest.
MikeOn 11/1/2011 8:33 AM, Werner Schroedinger werner.schroedinger*|*googlemail.com wrote:
Sent to CCL by: "Werner Schroedinger" [werner.schroedinger^-^googlemail.com] In some PDB protein structure I would like to study flexibility in some concrete part of the molecule (small loop). I would like to perform a) protein folding where all the protein is rigid except the selected part, which remains totally flexible b) molecular dynamics, where it is only flexible the previously selected part Although this approach could seem unrealistic, I would like to know which method/programs, etc, would you recommend for performing this.>