Posts list

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

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