Gianluca Interlandi

Hi Andreas, Thanks for your reply. 3) I'll set something up, hopefully this week. 3gxb is a dimer in the PDB, but I assume you want the monomer? The PDB file that I uploaded here: http://gianluca.today/Files/Campari/ is a monomer. If you want to use directly the PDB file deposited with PDB code 3GXB, then I would use chain A. Best, Gianluca Gianluca Interlandi, PhD gianluca@u.washington.edu +1 (206) 685 4435 http://gianluca.today/ Research Assistant Professor at the Department of Bioengineering at...

Hi Andreas, Thanks for your answers. If you don't mind, I have more questions: 1) Do you have some citations about your protein docking studies with CAMPARI? That would be helpful. 2) What distance does -30kcal/mol per group roughly correspond to? Is it similar to CHARMM22 10-12 LJ cutoff with switching? 3) I would be interested in synergizing. But, I would like to get first an estimate of the performace. For example, to do rigid-body docking of the following two globular proteins. How long would...

Dear CAMPARI developers and users, I have a few questions concerning CAMPARI/ABSINTH: 1) Has CAMPARI ever been used to model the complex of two globular protein domains by treating them as rigid bodies? 2) In the ABSINTH paper (2009) I read that "it is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions". Is there any evidence , or arguments in favor, that ABSINTH would correctly describe the complex between...