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General discussions (Q&As) / Re: Base Stacking analysis
« on: June 26, 2014, 12:08:26 am »
Hi Xiang-Jun,
Could you explain more about the algorithm of base stacking area analysis?
1. What is the mean base-pair plane?
2. How to project the “exocyclic atoms”?
3. As you mentioned “not too far away”, is there a threshold for stacking determination in your algorithm? And what is it?
4. How do you think the relation between stacking areas and stacking energy? Do you know any software out there for direct stacking energy estimations?
Best regards,
starcpw
Could you explain more about the algorithm of base stacking area analysis?
1. What is the mean base-pair plane?
2. How to project the “exocyclic atoms”?
3. As you mentioned “not too far away”, is there a threshold for stacking determination in your algorithm? And what is it?
4. How do you think the relation between stacking areas and stacking energy? Do you know any software out there for direct stacking energy estimations?
Best regards,
starcpw