There are several good template structures for our target protein but, although it is known that a disulfide can form between a specific pair of cysteines in theses proteins (cysteines conserved in templates & target), the known structures show these cyteines as 15-20 angstroms apart. Nearby flexible loops or "hinge" regions can be identified. Would it be reasonable to model the target directly with a disulfide patch, or better to obtain an initial model based on the templates and then do more thorough MD/SA cycles with a restricted region of the model and S-S distance restraints before final refinement with the disulfide patch?
Thanks,
Tom Duncan -- Thomas M Duncan Research Associate Professor Dept Biochemistry & Molecular Biology Institute for Human Performance, Rm 4311 SUNY Upstate Medical University 750 E Adams St Syracuse, NY 13210