From 8cf95bffed4f95de75a62151e149386ad6d27ab2 Mon Sep 17 00:00:00 2001 From: dylanyang Date: Thu, 12 Nov 2026 09:48:08 +0900 Subject: [PATCH] README: Zenodo DOI badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 3da2e1d..7088266 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ License: Apache 2.0 Python >= 3.10 Install with conda + DOI

RFoldSearch enables fast RNA tertiary-structure search with 3Dr, a learned discrete structural alphabet. Each nucleotide is described by a 17-D vector: the rigid-body transform to its nearest non-sequential spatial neighbour and its local context. A VQ-VAE quantises this vector into one of 80 states, converting RNA chains into token strings. Targets sharing at least two token k-mers on a common diagonal with the query pass the prefilter, and the top N are aligned by affine-gap token Smith-Waterman, which gives the alignment score and the nucleotide correspondence. For the default search mode, RFoldSearch estimates token-alignment E-values using a database-specific Gumbel model followed by calibration of unrelated background counts. Hits are ranked by a structure score that combines the token-alignment score with the structural similarity of the aligned nucleotides, independently of the reported E-value. RFoldSearch-TM instead ranks candidates by US-align TM-score and does not report token-alignment E-values.