473 citations · 911 across the 17 of their papers we have counts for
8 papers · 1 filter
Automated RNA structure prediction uncovers a missing link in double glycine riboswitches
Wipapat Kladwang, Fang-Chieh Chou, Rhiju Das
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges b…
The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments
Pablo Cordero, Julius Lucks, Rhiju Das
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA s…
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
Fang-Chieh Chou, Parin Sripakdeevong, Sergey M. Dibrov +2
Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems,…
Can biopolymer structures be sampled enumeratively? Atomic-accuracy RNA loop modeling by a stepwise ansatz
Parin Sripakdeevong, Wipapat Kladwang, Rhiju Das
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realisti…
Two-dimensional chemical mapping for non-coding RNAs
Wipapat Kladwang, Christopher C. VanLang, Pablo Cordero +1
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic muta…
Why Can't We Predict RNA Structure At Atomic Resolution?
Kyle Beauchamp, Parin Sripakdeevong, Rhiju Das
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines curr…