Rhiju Das

A hydrogel bead-based platform for quantitative functional characterization of large protein libraries

Daria Passow, Polly Fordyce, Steven Banik, Rhiju Das et autres

De novo design of RNA pseudoknots with deep learning

Jill Townley, Wipapat Kladwang, David Baker, Hamish M Blair et autres

RNA design has been hindered by the limited accuracy of 3D structure prediction. Here, we show that intricate RNA structures can be generated with current deep learning tools through accurate de novo design of pseudoknot secondary structures. In an Eterna competition involving …

us, gb (code pays fourni par la source)

Cryo-EM of a nucleotide-polymerizing ribozyme enables its predictive improvement

Deni Szokoli, Hingey JH, Yuan Wu, Daniel B. Haack et autres

Abstract Ribozymes capable of self-replication from nucleotides would have been central to the hypothesized RNA World. The leading laboratory models for such molecules were converted from a class I ligase by in vitro evolution but then developed without 3D structures. Here, scaffolded …

us (code pays fourni par la source)

OpenKnotAI: code for RNA library design, SHAPE data processing, OpenKnot scoring, and RNA design methods

Jill Townley, Wipapat Kladwang, David A. Baker, H. Blair et autres

Code accompanying the OpenKnotAI study, “De novo design of RNA pseudoknots with deep learning” (preprint: https://doi.org/10.64898/2026.05.21.726960). This deposit bundles source-only snapshots (Git history removed) of the software used for RNA library design, SHAPE chemical-mapping data processing, OpenKnot scoring, and the RNA sequence/structure …

us, gb (code pays fourni par la source)

OpenKnotAI: code for RNA library design, SHAPE data processing, OpenKnot scoring, and RNA design methods

Jill Townley, Wipapat Kladwang, David A. Baker, H. Blair et autres

Code accompanying the OpenKnotAI study, “De novo design of RNA pseudoknots with deep learning” (preprint: https://doi.org/10.64898/2026.05.21.726960). This deposit bundles source-only snapshots (Git history removed) of the software used for RNA library design, SHAPE chemical-mapping data processing, OpenKnot scoring, and the RNA sequence/structure …

us, gb (code pays fourni par la source)

eternagame/OpenKnotAIDesignData: v4.5.2 — M2 single-mutant SHAPE data

Rhiju Das

Add `OK7a_M2_data.v4.5.2.csv`: mutate-and-map (M2) SHAPE data on single-nucleotide mutant libraries for all 20 Round 3 targets × 8 design methods (~100 mutants per design, 14,136 sequences total; median 98 mutants per design, range 52–100). Probed with 2A3 SHAPE (Ultima sequencing, 2025-09-04). Unlike …

us (code pays fourni par la source)

eternagame/OpenKnotAIDesignData: v4.5.2 — M2 single-mutant SHAPE data

Rhiju Das

Add `OK7a_M2_data.v4.5.2.csv`: mutate-and-map (M2) SHAPE data on single-nucleotide mutant libraries for all 20 Round 3 targets × 8 design methods (~100 mutants per design, 14,136 sequences total; median 98 mutants per design, range 52–100). Probed with 2A3 SHAPE (Ultima sequencing, 2025-09-04). Unlike …

us (code pays fourni par la source)

Struct2SeQ designed RNA molecule

Adamo S. Mancino, Hingey JH, Shujun He, Daniel B. Haack et autres

EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

MPNN-RFdiff designed RNA molecule

Hingey JH, Nicholas Spellmon, Andrew Favor, Andrew Kubaney et autres

EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

gRNAde designed RNA molecule

Nicholas Spellmon, Daniel B. Haack, Chaitanya K. Joshi, Boris Rudolfs et autres

EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.

Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle

Sebastian Balch, Elsa Franco-Echevarría, George E. Ghanim, Rachael C. Kretsch et autres

In most eukaryotes, the reverse transcriptase telomerase counteracts telomere shortening by processively adding telomeric DNA repeat sequences to chromosome ends. Telomerase activity depends on the telomerase reverse transcriptase (TERT) and the telomerase RNA (hTR in humans). Processive telomere elongation is critical for …

gb, us (code pays fourni par la source)

Template-based RNA structure prediction advanced through a blind code competition

Youhan Lee, Shujun He, Toshiyuki Oda, G Gangadhareswar Rao et autres

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previously unreleased structures to tackle this challenge. The top three submitted algorithms achieved scores …

us, se, cn, fr, gb, de, it, ae, jp, uy (code pays fourni par la source)