Posts list

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

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