Posts list

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

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