I’m intrigued by the prospect of using AMPLE to test multiple distant homologs in a MR problem. I’ve used HHPRED to identify about 20 high-probability homologs of known structure, each of which has about 20-25% identity with the unknown protein. However, it’s not clear to me from the documentation whether the program will use the alignments from HHPRED, and, if so, how I should provide that information.
Or does AMPLE perform its own alignment? I.e., do I simply point the program to a directory containing 20 different PDB files and stand back? Thanks for any insights. Cheers, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu
