The algorithm and the website for "DSSR-enabled identification, annotation, and visualization of G-quadruplexes" (http://g4.x3dna.org/) have recently been updated and polished. In addition to the list of all G4s in the PDB ( http://g4.x3dna.org/DSSR-G4DB.html), the website also allows users to upload their own structures in PDB or mmCIF format for on-demand processing.
As an example, see the output from DSSR on PDB entry 8taa ( http://g4.x3dna.org/pdb/8taa/index.html). ``` *List of 4 G-tetrads* 1 glyco-bond=---- sugar=---- groove=---- planarity=0.121 type=planar O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.091 type=planar O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 4 glyco-bond=---- sugar=---- groove=---- planarity=0.121 type=planar O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25 *List of 1 G4-helix In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity,* * and may contain more than one G4-stem. Helix#1, 4 G-tetrads, INTRA-molecular, with 1 stem* 1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25 step#1 mp(<<,backward) area=11.87 rise=3.23 twist=-26.3 step#2 mm(<>,outward) area=28.76 rise=3.31 twist=-9.9 step#3 pm(>>,forward) area=8.87 rise=3.34 twist=32.5 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,A.DG21,A.DG22 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG7,A.DG18,A.DG19 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG9,A.DG10,A.DG15,A.DG16 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG12,A.DG1,A.DG24,A.DG25 *List of 1 G4-stem In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along* * each of the four strands. Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)* 1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25 step#1 pm(>>,forward) area=8.87 rise=3.34 twist=32.5 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG18,A.DG19 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG21,A.DG22 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG24,A.DG25 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT17 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT20 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT23 ``` I welcome your comments and suggestions for further improvement of the resource. Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Director, X3DNA-DSSR NIGMS National Resource Email: xiang...@x3dna.org 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/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
