Using UCSF Chimera, re-obtain the structure of the complex (1ABE).This file will be used in the next part for the generation of the surface and spheres. Using UCSF chimera, delete hydrogen atoms from the protein and save this receptor structure as a PDB file.Note that if the side-chain with missing atoms is close to the binding site, its replacement with Gly will affect results consider manual replacement with Ala or manual rebuilding of the residue. Thus steps e) and f) in the UCSF tutorial are obsolete and you can directly proceed to write the MOL2 file. UCSF Chimera also check for incomplete residues and automatically change these to glycines. This involves deleting ligand and solvent molecules, elimination alternate locations of residues, change of selenomethionines to methionines, adding hydrogen atoms, and assigning charges to protein atoms. Using UCSF Chimera, prepare the structure of the receptor for docking.Using UCSF Chimera, obtain and examine the structure of L-arabinose-binding protein (1ABE).The list below will serve as a guide to the overall work flow, and suggests which option to follow. The UCSF tutorial is rather comprehensive and sometimes offers multiple ways of performing a task. You will find details on how to accomplish each of the tasks listed below by carefully reading her tutorial. Therese Lang, a graduate student at UCSF. The DOCK website has a nice tutorial prepared by P.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. Archives
March 2023
Categories |