Midterm
Outcomes:
- Develop functional familiarity with molecular dynamic simulation
procedures.
- Develop and understanding of the molecular refinement procedure..
Objectives:
Obtain and refine structure of 1RWD and report the structure with
lowest bb rmsd
with respect to 1BRF. Note that 1RWD is the structure of bb only;
sidechains need to be completed.
Details:
Using the Xplor-NIH perform iterations of
melting/cooling/minimization of the starting 1RWD structure in order to
obtain a new minimized structure with sidechains completed. You may
work in groups of two people per team.
Submit:
- All requried files to repeat your procedure including sequences,
xplor scripts or other scripts developed by your team
- The PDB file of the refined structure that exhibits the least bb
and sidechain rmsd with 1BRF.
- A completed profession report in the template provided below
- Your report needs to consists of Abstract, Introduction,
Material/Methods, Results and Conclusion section. Inclusion of
references is highly recommended.
- Your report should include a flowchart or step-by-step
description of your protocol
Required Material:
Structure of 1RWD
Spreadsheet of 1RWD dihedrals
1RWD sequence
Perl script to convert a list of
backbone dihedrals to Xplor restraints tables
Xplor script to create an extended
structure
Report template in MS
format or OpenOffice
format
Bibus
or Zotero bibliography software
Example minimization routine
with fixed backbone and an iterating loop
Example minimization routine with
backbone dihedral restraints and an iterating loop