The website http://g4.x3dna.org for the DSSR annotated G-quadruplexes (G4) in the PDB has been launched. Here are two examples showcasing G4 features automatically derived by DSSR: http://g4.x3dna.org/entries/6r9l and http://g4.x3dna.org/entries/5ua3
The 3DNA-DSSR program detects and annotates G4 structures from atomic coordinates in PDB or PDBx/mmCIF format. It identifies G-tetrads and arranges them into G4 helices, composed of G4 stems via coaxial stacking interactions. G4 stems are categorized by loops connecting the four strands, and by common names [e.g., chair, basket] or the Webba da Silva nomenclature [e.g., 3(-P-Lw-Ln) for 2GKU]. DSSR accounts for bugles along a strand, characterizes G4 structures using rigid-body parameters (including Rise and Twist), and quantifies stacking by overlapping areas. The program also introduces a novel schematic representation, highlighting G-tetrads using square blocks (to render in PyMOL). I've have been actively developing and refining the DSSR module for G4 structures for more than two years. I greatly appreciate your comments or suggestions. Best regards, Xiang-Jun [This announcement is cross-posted on PDB-l and CCP4BB] -- Xiang-Jun Lu (Ph.D.) Email: [email protected] Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
