69 citations · 76 across the 7 of their papers we have counts for
7 papers
Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-seq Protocol
Matthew G. Seetin, Wipapat Kladwang, J. P. Bida +1
Chemical mapping methods probe RNA structure by revealing and leveraging correlations of a nucleotide's structural accessibility or flexibility with its reactivity to various chemi…
A mutate-and-map protocol for inferring base pairs in structured RNA
Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang +1
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resoluti…
Quantitative DMS mapping for automated RNA secondary structure inference
Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang +1
For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inf…
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…