Hallo Modellers!
I try to model protein binding sites including ligand information in terms of distance dependent atom pair potentials.
For testing this approach I tried to predict the orientations of binding site residues. After generating 100 models of a protein I compare them with the actual crystal structures. The predictions are quite reasonable. However, there seem to be some problems in the side chain conformations of the aromatic amino acids (maybe because of steric hinderance). In some cases there is only one preffered conformation of, e.g. a tyrosine, i.e. only one preffered value of the CHI1 dihedral angle.
I have read in the manual that there is the possibility to ROTATE_DIHEDRALS by randomizing. How do I have to set up my top file to tell MODELLER to select certain amino acids (e.g. by number) and to randomize the CHI1 and/or CHI2 angles and - if possible - to generate models with diverse CHI1 and/or CHI2 angles, even if some are not energetically favourable? The rest of the protein should be modelled as usual.
Do you think this procedure an advisable way to do or do you have any better idea how I can constrain the modelling process to generate more diverse dihedral angles for selected amino acids?
Thank you for your answer,
nice regards,
Andreas
-- ###################################################################### # Andreas Evers # # # # Research group for Drug Design & X-ray Crystallography # # Institute of Pharmaceutical Chemistry # # Philipps-University of Marburg # # Marbacher Weg 6 phone2 +49-6421-28-25072 # # D-35032 Marburg FAX: +49-6421-28-28994 # # email: Andreas.Evers@mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ######################################################################