Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures

By Guohui Zheng, Xiang-Jun Lu, Wilma K. Olson. Nucleic Acids Res., 2009

318 citations recorded by the source corpus.

The w3DNA (web 3DNA) server is a user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their complexes with proteins and other ligands. The server allows the user to determine a wide variety of conformational parameters in a given structure—such as the identities and rigid-body parameters of interacting nucleic-acid bases and base-pair steps, the nucleotides comprising helical fragments, etc. It is also possible to build 3D models of arbitrary nucleotide sequences and helical types, customized single-stranded and double-helical structures with user-defined base-pair parameters and sequences, and models of DNA ‘decorated’ at user-defined sites with proteins and other molecules. The visualization component offers unique, publication-quality representations of nucleic-acid structures, such as ‘block’ images of bases and base pairs and stacking diagrams of interacting nucleotides. The w3DNA web server, located at http://w3dna.rutgers.edu, is free and open to all users with no login requirement.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/75c0e2556f72a4e7928f25c0db05c3f6b3d01e41

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (2019, methodology): “The original w3DNA server (14) used a fixed list of modified nucleotides mapped to their canonical counterparts.”