Dear Modellers, Though there are many problems in modeling the loop regions, but even when there is no insertion in the loop region and is devoid of any higher order localized structural topology, the loop residues are just connectors. Here also i am seeing some problem. Even when the periphery is at a minimal distance threshold to native state making the GDT_TS or even GDT_HA very high, the RMSD i found was much more than expectation. So the model scrutiny revealed the complexity in the loop region.
SO IS THERE ANY SCRIPT IN MODELLER WHICH REFINES ALL LOOP CONNECTORS THROUGH MD CONJUGATED GRADIENT, MAKING THE RMSD ALSO DROOP DOWN AS IS THE CASE FOR GDT OR TM-SCORE.
Thanks a lot, Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA