Posts list

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

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