Posts list

  1. Citations to 3DNA publications in the Web of Science · 2020-07-01
  2. Over 5000 registrations on the 3DNA Forum · 2020-06-26
  3. Cover images of the RNA Journal in 2020 · 2020-06-15
  4. Paper on DSSR-PyMOL schematics · 2020-05-22
  5. Context-aware in silico base mutations enabled by DSSR 2.0 · 2020-05-11
  6. May's article on "The Best Ways to Study DNA and Protein Interactions" · 2020-05-10
  7. DSSR is cited in a Nature paper on RIC-seq for profiling RNA–RNA interactions · 2020-05-10
  8. SARS-CoV-2, RNA G-Quadruplexes and 3DNA · 2020-04-13
  9. SNAP for the analysis of TF-DNA complexes containing 5-methyl-cytosines · 2019-12-20
  10. 3DNA-DSSR is linked in the G4-society website · 2019-12-13
  11. 3DNA/blocview-PyMOL images in covers of the RNA journal · 2019-12-06
  12. Web API to 3DNA · 2019-11-21
  13. DSSR-enhanced visualization of nucleic acid structures in PyMOL · 2019-10-22
  14. SNAP and DSSR in DNAproDB · 2019-10-19
  15. ONZ classification of G-tetrads · 2019-10-15
  16. H-bonds reported by DSSR and SNAP · 2019-09-13
  17. DSSR is used in RNAMake and 3dRNA 2.0 · 2019-09-02
  18. 5CM and 5MC, two forms of 5-methylcytosine in the PDB · 2019-08-05
  19. R wrapper to DSSR in VeriNA3d · 2019-07-27
  20. Web 3DNA 2.0 is highlighted in the NAR'19 web server cover · 2019-06-28
  21. DNA conformational changes play a force-generating role during bacteriophage genome packaging · 2019-06-04
  22. The article on G.A pairs in ACS Biochemistry · 2019-06-03
  23. Web 3DNA 2.0 paper published in NAR · 2019-06-03
  24. 3DNA blocview image in the cover of the RNA journal · 2019-05-27
  25. DSSR is used for the analysis of CRISPR PbuCas13b-crRNA · 2019-04-03
  26. DSSR on PDB entry 6neb · 2019-02-21
  27. Non-G base tetrads · 2019-02-19
  28. G-tetrad and pseudo G-tetrads · 2019-02-16
  29. Starting DNA or RNA structures · 2019-02-12
  30. misc tips and tricks · 2018-12-20
  31. Identification of nucleotides · 2018-11-15
  32. Mutations to 3-methyladenine · 2018-11-07
  33. DSSR in the visualization of DNA/RNA structures · 2018-10-28
  34. Enhanced features in DSSR for G-quadruplexes · 2018-10-21
  35. DSSR is fast for MD analysis · 2018-10-17
  36. Integrations of DSSR to other bioinformatics resources · 2018-05-11
  37. DSSR-enabled cartoon block images for G-quadruplex · 2018-05-11
  38. Over 10K nucleic-acid-containing structures in the PDB · 2018-05-11
  39. One base forming two Watson-Crick pairs? · 2018-04-08
  40. DNA conformational changes may play an active role in viral genome packaging · 2018-03-31
  41. Handling of abasic sites in DSSR · 2017-11-16
  42. Stem, helix, and coaxial stacking in DSSR · 2017-11-15
  43. Base stacks in non-stem regions · 2017-11-14
  44. Identification and characterization of G-quadruplexes · 2017-11-13
  45. Detection of multiplets in DSSR · 2017-11-12
  46. DSSR-Jmol featured in cover image of NAR'17 web-server issue · 2017-06-30
  47. SNAP is cited in the DNAproDB paper · 2017-05-15
  48. DSSR-Jmol paper in NAR · 2017-05-05
  49. DSSR in the structural analysis of an E.coli initiator tRNAfMet A1-U72 variant · 2017-04-18
  50. Weird PDB entries · 2016-11-28
  51. Highlights of recent developments of 3DNA/DSSR · 2016-11-20
  52. Pauling's triplex model of nucleic acids is available in 3DNA · 2016-11-16
  53. 3DNA fiber models · 2016-09-23
  54. PyMOL wrapper to 3DNA fiber models · 2016-09-23
  55. 3DNA C source code is available · 2016-09-06
  56. DSSR is used in the URS DataBase · 2016-05-30
  57. DSSR in the validation of NMR RNA structures · 2016-04-21
  58. The DSSR --block-color option · 2016-04-01
  59. Cartoon-block representation of quadruplex-duplex interface · 2016-02-16
  60. Integrating DSSR into Jmol and PyMOL · 2016-01-27
  61. Characterization of base-pair geometry · 2016-01-21
  62. DSSR base blocks in PyMOL, interactively · 2016-01-21
  63. 3DNA Forum is spam free · 2016-01-16
  64. Ask reproducible questions, publicly · 2016-01-11
  65. Details on the simple base-pair parameters · 2016-01-10
  66. Fitting of base reference frame · 2016-01-07
  67. Automatic identification of nucleotides · 2016-01-05
  68. 'Simple' parameters for non-Watson-Crick base pairs · 2016-01-01
  69. Identification of multiplets in DSSR · 2015-12-28
  70. Quality control of DSSR (3DNA) source code · 2015-12-27
  71. First mention of SNAP in a peer-reviewed journal article · 2015-12-24
  72. First citation to the DSSR NAR paper in JMB · 2015-11-24
  73. Metallo-base pairs can be identified by DSSR · 2015-11-12
  74. Citation statistics to 3DNA publications · 2015-11-07
  75. Jmol and DSSR · 2015-10-14
  76. Analyzing DNA/RNA structures with Curves+ and 3DNA · 2015-10-13
  77. DSSR --symmetry/--nmr options and MODEL/ENDMDL ensemble · 2015-10-10
  78. The 3DNA mutate_bases program is cited in Nature · 2015-10-10
  79. Parsing DSSR json output · 2015-09-06
  80. Simple base-pair parameters · 2015-09-04
  81. Updates on x3dna.org · 2015-09-03
  82. Output of reference frames in DSSR JSON output · 2015-09-03
  83. Quantifying base-pair geometry by six rigid-body parameters · 2015-09-01
  84. DSSR output in JSON format · 2015-08-27
  85. DSSR has been published, and its results are reproducible · 2015-07-24
  86. Conformation of the sugar ring in nucleic acid structures · 2015-06-11
  87. The DSSR --prefix and --cleanup options · 2015-06-10
  88. Assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format · 2015-05-22
  89. The value of tiny and self-contained software in the big-data era · 2015-05-13
  90. Open invitation on writing a DSSR plugin for PyMOL · 2015-05-10
  91. Ambiguous 'analyze' and 'rebuild' program names · 2015-05-08
  92. Name of base atoms in PDB formats · 2015-05-04
  93. Nucleic acid structures in the RCSB PDB · 2015-04-09
  94. The do_x3dna paper by Kumar and Grubmuller in Bioinformatics · 2015-04-07
  95. Modified pseudouridines · 2015-03-11
  96. Exterior loop in RNA secondary structure · 2015-02-22
  97. DSSR-derived DBN for an input entry with multiple RNA molecules · 2015-02-11
  98. The Biophysical Society (BPS) 59th annual meeting at Baltimore · 2015-02-04
  99. Weird atom names of ligand thiamine pyrophosphate (TPP) · 2015-02-04
  100. The 3DNA Forum registered users have reached 2000 · 2015-02-03
  101. Characterization of H-type pseudoknots with DSSR · 2015-01-31
  102. Two more citations to DSSR · 2014-12-22
  103. Processing large structures in mmCIF format · 2014-10-13
  104. DNA/RNA molecular dynamics trajectory analysis with do_x3dna · 2014-09-03
  105. List of modified nucleotides in DSSR output · 2014-08-24
  106. DSSR-derived secondary structure in BPSEQ format · 2014-08-12
  107. RNA pseudoknot detection and removal with DSSR · 2014-08-10
  108. Get hydrogen bonds with DSSR · 2014-04-11
  109. DSSR for Windows, one executable fits all · 2014-04-10
  110. Draw DSSR-derived RNA secondary structures in ct format · 2014-03-25
  111. DSSR now has a user manual! · 2014-03-12
  112. DSSR-derived secondary structure in .ct format · 2014-02-05
  113. Single- and double-stranded Zp · 2013-11-20
  114. Weird cases of nucleotides with missing atoms · 2013-11-20
  115. Three citations to 3DNA in the November 2013-41(21) issue of NAR · 2013-11-20
  116. 3DNA/DSSR runs just fine under Mac OS X Mavericks · 2013-10-31
  117. DSSR works perfectly under DOS (in native Windows) · 2013-10-25
  118. DSSR command-line processing · 2013-10-24
  119. Modified nucleotides in the PDB · 2013-10-18
  120. Different names for the methyl group in DNA and RNA structures · 2013-10-17
  121. Citations to the 3DNA homepage · 2013-10-16
  122. Compiling ViennaRNA on Mac OS X · 2013-10-11
  123. Web-interface to DSSR · 2013-09-10
  124. UNR- and GNRA-type U-turns · 2013-09-09
  125. Restraint optimization of DNA backbone geometry using PHENIX · 2013-09-06
  126. Detection of helical junctions in nucleic acid structures · 2013-09-04
  127. Drawing an RNA secondary structure from its 3D coordinates · 2013-09-01
  128. 3DNA forum registrations pass 1000 · 2013-06-27
  129. DSSR identifies kink-turns! · 2013-06-26
  130. 3DNA JoVE paper published · 2013-05-03
  131. DSSR, what is it and why bother? · 2013-03-29
  132. Number of base pairs with at least two inter-base H-bonds: 28 or 29? · 2012-12-03
  133. The Calcutta U-U base pair · 2012-11-30
  134. Analysis of molecular dynamics simulations trajectories · 2012-11-28
  135. Application of the mutate_bases program in inferring statistical protein-DNA potentials · 2012-10-26
  136. Quantification of base-stacking interactions using overlap area · 2012-10-21
  137. Named base pairs · 2012-10-07
  138. Unusual glycosidic bond in nucleic acid structures in the PDB/NDB · 2012-10-06
  139. FRETmatrix: a methodological platform for the simulation and analysis of FRET in nucleic acids · 2012-09-21
  140. The number of 3DNA forum registrations has reached 500 · 2012-09-16
  141. Classification of dinucleotide steps into A- and B- and TA-DNA · 2012-09-07
  142. Four papers in the August 2012 [40(14)] issue of NAR cite 3DNA · 2012-08-11
  143. Rectangular block expressed in PDB format · 2012-08-04
  144. Effect of reversing strands of a DNA duplex on 3DNA calculated parameters · 2012-08-02
  145. Schematic diagrams of base-pair parameters · 2012-08-01
  146. Perl scripts are obsolete but still available · 2012-07-31
  147. Specification of base pairs in 3DNA · 2012-07-30
  148. Is the O2′(G)...O2P(U) H-bond in GpU platforms real? · 2012-06-12
  149. Reverse Watson-Crick base pairs · 2012-06-11
  150. Hoogsteen and reverse Hoogsteen base pairs · 2012-06-08
  151. Rectangular block expressed in MDL molfile format · 2012-05-03
  152. Difference in shear of neighboring base pairs affects twist angle · 2012-04-30
  153. blocview: a simple, effective visualization tool for DNA/RNA structures · 2012-04-28
  154. Rectangular block representation of base-pairs in 3DNA · 2012-04-27
  155. Two slightly different definitions of sugar pucker · 2012-04-27
  156. Building a bridge between Curves+ and 3DNA · 2012-04-26
  157. Torsion angles of nucleic acid structures · 2012-04-23
  158. How to calculate torsion angle? · 2012-04-22
  159. Pseudo-torsions to simplify the representation of DNA/RNA backbone conformation · 2012-04-21
  160. Definition of the chi (χ) torsion angle for pseudouridine · 2012-04-17
  161. The chi (χ) torsion angle characterizes base/sugar relative orientation · 2012-04-16
  162. Sugar pucker correlates with phosphorus-base distance · 2012-04-10
  163. GpU dinucleotide platform, the smallest unit with key RNA structural features · 2012-04-10
  164. Least-squares fitting procedures with illustrated examples · 2012-04-04
  165. Seeing is understanding as well as believing · 2012-04-03
  166. Generating idealized A-form RNA structures of generic sequence · 2012-03-30
  167. Does 3DNA work for RNA? · 2012-03-06
  168. About 3DNA · 2012-02-28
  169. Outside links · 2012-02-26
  170. Credits · 2012-02-21
  171. New features in 3DNA v2.1 · 2012-02-11
  172. What's special about the GpU dinucleotide platform? · 2012-01-10
  173. What find_pair in 3DNA can do · 2012-01-10
  174. Curves+ vs 3DNA · 2012-01-10

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