Developing Community Resources for Nucleic Acid Structures
Overview
Affiliations
In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.
Advances and Mechanisms of RNA-Ligand Interaction Predictions.
Zhuo C, Zeng C, Liu H, Wang H, Peng Y, Zhao Y Life (Basel). 2025; 15(1).
PMID: 39860045 PMC: 11767038. DOI: 10.3390/life15010104.
FURNA: A database for functional annotations of RNA structures.
Zhang C, Freddolino L PLoS Biol. 2024; 22(7):e3002476.
PMID: 39074139 PMC: 11309384. DOI: 10.1371/journal.pbio.3002476.
Incorporating Sequence-Dependent DNA Shape and Dynamics into Transcriptome Data Analysis.
Kalsan M, Jabeen A, Ahmad S Methods Mol Biol. 2024; 2812:317-343.
PMID: 39068371 DOI: 10.1007/978-1-0716-3886-6_18.
The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.
Lawson C, Berman H, Chen L, Vallat B, Zirbel C Nucleic Acids Res. 2023; 52(D1):D245-D254.
PMID: 37953312 PMC: 10767938. DOI: 10.1093/nar/gkad957.
RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures.
Malhotra S, Mulvaney T, Cragnolini T, Sidhu H, Joseph A, Beton J Nucleic Acids Res. 2023; 51(18):9567-9575.
PMID: 37670532 PMC: 10570027. DOI: 10.1093/nar/gkad721.