Posts list

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

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