Effect of reversing strands of a DNA duplex on 3DNA calculated parameters

From a pure structural perspective, the designation of the two strands in an anti-parallel DNA duplex is sort of arbitrary. Thus, for a given PDB file, let’s assume that the atomic coordinates of chain A (strand I) come before those of chain B (strand II). We can swap the order of the two chains as they appear in the PDB file, i.e., list first the atomic read more

Comment

---

Perl scripts are obsolete but still available

As of v2.1, I’ve switched from Perl to Ruby as the scripting language for 3DNA. Consequently, the Perl scripts in previous versions of 3DNA (v1.5 and v2.0) are now obsolete. I’ll only correct bugs in existing Perl scripts, but will not add any new features.

For back reference, the scripts are still available from a separate directory $X3DNA/perl_scripts, read more

Comment

---

Specification of base pairs in 3DNA

In 3DNA, each base pair (bp) is specified by the identity of its two comprising nucleotides (nts), and their interactions. Some examples are shown below based on the PDB entry 1ehz (the crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution), with the shorthand form on the right:

....>A:...1_:[..G]G-----C[..C]:..72_:A<....  G-C
....>A:read more

Comment

---

Seeing is understanding as well as believing

As the old saying goes, a picture is worth a thousand words. To help you have a better idea of what 3DNA/DSSR is about, we’ve collected the following pictures; they serve to demonstrate selected features from 3DNA/DSSR’s versatile functionality.

read more

Comment [1]

---

Welcome

A video overview of DSSR

DSSR (Dissecting the Spatial Structure of RNA) is an integrated software tool for the analysis/annotation, model building, and schematic visualization of 3D nucleic acid structures (see the figures below and the video overview). It is built upon the well-known, tested, and trusted 3DNA suite read more

---

Outside links

The following links point to tools that are relevant to 3DNA.

  • Curves+ — an updated version of the well-known Curves program, and it conforms to the standard base reference frame.
  • 3D-DART — 3DNA-Driven DNA Analysis and Rebuilding Tool. Another web-interface to commonly used 3DNA functionality.
  • do_x3dna — “
  • read more

Comment

---

New features in 3DNA v2.1

The v2.1 release of 3DNA, currently in beta, contains many refinements of existing C programs, a complete migration from Perl scripts to Ruby, and additions of several significant new programs. All know bugs in v2.0 have been fixed. Highlights include:

  • Added mutate_bases to perform in silico base mutations in nucleic-acid-containing structures (DNA,
  • read more

Comment

---

· Newer »

Thank you for printing this article from http://x3dna.org/. Please do not forget to visit back for more 3DNA-related information. — Xiang-Jun Lu