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Topics - eswright

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RNA structures (DSSR) / Avoiding pairing that cross chains
« on: July 26, 2019, 01:11:05 pm »
I used DSSR to calculate the secondary structure of PDB 4V6W chain A5, which is a eukaryotic LSU rRNA. This resulted in 896 left pairings "(" and 880 right pairings ")". Presumably this imbalance is because some of the pairs are inter-chain. Is there a way to force pairings only within single chains (i.e., intra-chain pairs only)? Ideally, I would like to obtain a balanced structure for each chain by itself.


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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.