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  1. (hist) ‎2008 Spring ‎[0 bytes]
  2. (hist) ‎De Novo Design ‎[0 bytes]
  3. (hist) ‎2019 Covalent docking tutorial 1 with PDB 2VKG ‎[0 bytes]
  4. (hist) ‎Outdated Info ‎[13 bytes]
  5. (hist) ‎2020 DOCK tutorial 1 with PDBID XXXX ‎[16 bytes]
  6. (hist) ‎DOCK VS Parameters ‎[21 bytes]
  7. (hist) ‎Seawulf Programs Needed ‎[22 bytes]
  8. (hist) ‎DOCK VS Utilities ‎[31 bytes]
  9. (hist) ‎DOCK VS Utilities/Info ‎[31 bytes]
  10. (hist) ‎AMBER tricks ‎[35 bytes]
  11. (hist) ‎Coming Soon ‎[36 bytes]
  12. (hist) ‎DOCK GA Tutorials ‎[38 bytes]
  13. (hist) ‎INSPH ‎[47 bytes]
  14. (hist) ‎Showsph.in ‎[49 bytes]
  15. (hist) ‎DOCK CV Tutorials ‎[51 bytes]
  16. (hist) ‎Lab-designed code and programs ‎[55 bytes]
  17. (hist) ‎De Novo Design (DOCK DN) ‎[62 bytes]
  18. (hist) ‎Gnuplot ‎[84 bytes]
  19. (hist) ‎2020 AMS-536 Spring ‎[90 bytes]
  20. (hist) ‎Making images for publication ‎[91 bytes]
  21. (hist) ‎Showbox.in ‎[99 bytes]
  22. (hist) ‎DOCK DN Utilities ‎[99 bytes]
  23. (hist) ‎DOCK DN Utilities/Info ‎[99 bytes]
  24. (hist) ‎Ghostscript ‎[103 bytes]
  25. (hist) ‎Small Molecule Evolution (DOCK GA) ‎[104 bytes]
  26. (hist) ‎DOCK GA Input File(s) ‎[104 bytes]
  27. (hist) ‎Config ‎[114 bytes]
  28. (hist) ‎CONGA ‎[115 bytes]
  29. (hist) ‎CONGA (CONstruction by Genetic Algorithm) ‎[115 bytes]
  30. (hist) ‎General Dock Utilities ‎[132 bytes]
  31. (hist) ‎General Dock Utilities/Info ‎[132 bytes]
  32. (hist) ‎Visiting BNL ‎[140 bytes]
  33. (hist) ‎Amber to pdb ‎[148 bytes]
  34. (hist) ‎Rename files in Unix ‎[169 bytes]
  35. (hist) ‎Make surface ‎[173 bytes]
  36. (hist) ‎Get Job ids to use for llcancel ‎[181 bytes]
  37. (hist) ‎Legacy Info ‎[188 bytes]
  38. (hist) ‎Gdb (GNU Debugger) ‎[201 bytes]
  39. (hist) ‎Archiving old data ‎[203 bytes]
  40. (hist) ‎Get time for job completion ‎[206 bytes]
  41. (hist) ‎Common Errors - ctrl M ‎[207 bytes]
  42. (hist) ‎Pdb to mol2 ‎[209 bytes]
  43. (hist) ‎Getting a BNL Account ‎[210 bytes]
  44. (hist) ‎Benchmarking ‎[221 bytes]
  45. (hist) ‎AMBER Lipid Tutorials ‎[232 bytes]
  46. (hist) ‎Which Unix Distribution? ‎[233 bytes]
  47. (hist) ‎Method development ‎[237 bytes]
  48. (hist) ‎Ethernet Cables ‎[244 bytes]
  49. (hist) ‎Valgrind ‎[252 bytes]
  50. (hist) ‎Reference.vmd.script ‎[270 bytes]
  51. (hist) ‎Wiki Editing ‎[271 bytes]
  52. (hist) ‎Example Input Files ‎[273 bytes]
  53. (hist) ‎DOCK Denovo ‎[285 bytes]
  54. (hist) ‎De novo DOCK ‎[285 bytes]
  55. (hist) ‎DOCK NOVA ‎[285 bytes]
  56. (hist) ‎NOVA ‎[285 bytes]
  57. (hist) ‎Influenza ‎[290 bytes]
  58. (hist) ‎X-Win32 ‎[297 bytes]
  59. (hist) ‎Unix find ‎[316 bytes]
  60. (hist) ‎Sphere Generation ‎[320 bytes]
  61. (hist) ‎Secure Shell (ssh) ‎[323 bytes]
  62. (hist) ‎Parameter List/Explanations ‎[327 bytes]
  63. (hist) ‎Submitting BlueGene Jobs ‎[336 bytes]
  64. (hist) ‎Drug-like organic molecules ‎[341 bytes]
  65. (hist) ‎Octave ‎[350 bytes]
  66. (hist) ‎Example scripts ‎[356 bytes]
  67. (hist) ‎Advanced Dock Utilities ‎[362 bytes]
  68. (hist) ‎Ways to remove the first line ‎[364 bytes]
  69. (hist) ‎BlueGene ‎[368 bytes]
  70. (hist) ‎Clustering in R ‎[378 bytes]
  71. (hist) ‎Using convert command unix ‎[379 bytes]
  72. (hist) ‎SB2011 testset ‎[379 bytes]
  73. (hist) ‎Advanced Dock Utilities/Information ‎[387 bytes]
  74. (hist) ‎Restraint.vmd.script ‎[390 bytes]
  75. (hist) ‎Histograms in R ‎[397 bytes]
  76. (hist) ‎Compiling Applications for BG/L ‎[402 bytes]
  77. (hist) ‎NOVA (Navigation and Optimization for Virtual Assembly) ‎[413 bytes]
  78. (hist) ‎De Novo Design (previously NOVA) ‎[413 bytes]
  79. (hist) ‎Blocked Standard Error of the Mean ‎[415 bytes]
  80. (hist) ‎Developer's Info ‎[427 bytes]
  81. (hist) ‎NAMD to mol2 ‎[437 bytes]
  82. (hist) ‎R - Statistical Computing ‎[444 bytes]
  83. (hist) ‎Get time estimate for free blocks ‎[445 bytes]
  84. (hist) ‎Release ‎[480 bytes]
  85. (hist) ‎General Dock Development Goals ‎[480 bytes]
  86. (hist) ‎Semester Checklist ‎[491 bytes]
  87. (hist) ‎Journal Articles from UCSF ‎[534 bytes]
  88. (hist) ‎DOCK Abbreviations Guide ‎[548 bytes]
  89. (hist) ‎SDF to mol2 ‎[555 bytes]
  90. (hist) ‎Amber to mol2 (protein) ‎[579 bytes]
  91. (hist) ‎Main Page ‎[588 bytes]
  92. (hist) ‎2016 AMBER tutorial with Thrombin ‎[614 bytes]
  93. (hist) ‎Joint Group Meeting 2011 ‎[631 bytes]
  94. (hist) ‎Footprint Plot Visualization ‎[648 bytes]
  95. (hist) ‎ZINC Database ‎[653 bytes]
  96. (hist) ‎ZINC12 Database ‎[653 bytes]
  97. (hist) ‎Vmd.rmsd.csh ‎[676 bytes]
  98. (hist) ‎Grid.in ‎[692 bytes]
  99. (hist) ‎VMD ‎[695 bytes]
  100. (hist) ‎HIV/AIDS ‎[702 bytes]
  101. (hist) ‎DOCK DN Tutorials ‎[741 bytes]
  102. (hist) ‎DOCK Release Objectives ‎[760 bytes]
  103. (hist) ‎Installing MSMS for VMD ‎[771 bytes]
  104. (hist) ‎Making images for publication using vmd ‎[786 bytes]
  105. (hist) ‎Cancer ‎[801 bytes]
  106. (hist) ‎Tutorials ‎[814 bytes]
  107. (hist) ‎NAMD tutorial ‎[833 bytes]
  108. (hist) ‎Disulfide.txt ‎[842 bytes]
  109. (hist) ‎Sed - Stream Editor in Unix ‎[852 bytes]
  110. (hist) ‎Remove waters from trajectories ‎[867 bytes]
  111. (hist) ‎DOCK GIST Parameters ‎[888 bytes]
  112. (hist) ‎2008-2009 LAB ‎[890 bytes]
  113. (hist) ‎2008 RCR GROUP MEETING ‎[890 bytes]
  114. (hist) ‎AMBER Tutorials ‎[892 bytes]
  115. (hist) ‎Optimize Polar Hydrogens ‎[902 bytes]
  116. (hist) ‎2010 GRD-500 Spring ‎[902 bytes]
  117. (hist) ‎Joint Group Meeting 2010 ‎[903 bytes]
  118. (hist) ‎2009-2010 GRD-500 Fall-Spring ‎[934 bytes]
  119. (hist) ‎Joint Group Meeting 2012 ‎[952 bytes]
  120. (hist) ‎2020 DOCK tutorial 4 with PDBID XXXX ‎[956 bytes]
  121. (hist) ‎Research Foundation ‎[973 bytes]
  122. (hist) ‎Setting up insurance through Research Foundation ‎[973 bytes]
  123. (hist) ‎Joint Group Meeting 2013 ‎[980 bytes]
  124. (hist) ‎DOCK CV Development Goals ‎[1,008 bytes]
  125. (hist) ‎Ptraj ‎[1,041 bytes]
  126. (hist) ‎Binding Footprint Program ‎[1,080 bytes]
  127. (hist) ‎DOCK GA Developer Progress ‎[1,083 bytes]
  128. (hist) ‎Energy Scoring Method in Grid ‎[1,088 bytes]
  129. (hist) ‎DOCK VS Tutorials ‎[1,088 bytes]
  130. (hist) ‎ZINC15 Database ‎[1,092 bytes]
  131. (hist) ‎Rizzo Lab Downloads ‎[1,157 bytes]
  132. (hist) ‎DOCK CV Benchmarking ‎[1,161 bytes]
  133. (hist) ‎AutoDock Vina Benchmark Results ‎[1,180 bytes]
  134. (hist) ‎Seawulf Cluster Assessment ‎[1,187 bytes]
  135. (hist) ‎PDFCreator ‎[1,195 bytes]
  136. (hist) ‎DOCK Tutorials ‎[1,294 bytes]
  137. (hist) ‎Pylab ‎[1,300 bytes]
  138. (hist) ‎2010 LAB ‎[1,307 bytes]
  139. (hist) ‎2010 RCR GROUP MEETING ‎[1,307 bytes]
  140. (hist) ‎No t4 step2 min.bash ‎[1,371 bytes]
  141. (hist) ‎With t4 step2 min.bash ‎[1,373 bytes]
  142. (hist) ‎Rotation students Wiki ‎[1,400 bytes]
  143. (hist) ‎LoadLeveler Chain Jobs ‎[1,408 bytes]
  144. (hist) ‎DOCK Compilation ‎[1,437 bytes]
  145. (hist) ‎2018 RCR GROUP MEETING ‎[1,442 bytes]
  146. (hist) ‎MOE ‎[1,469 bytes]
  147. (hist) ‎C Shell Scripting ‎[1,502 bytes]
  148. (hist) ‎How to purchase compounds for Rizzo lab ‎[1,541 bytes]
  149. (hist) ‎Fourier fit ‎[1,555 bytes]
  150. (hist) ‎CVS Commands ‎[1,677 bytes]
  151. (hist) ‎Dell 5110cn Printer ‎[1,700 bytes]
  152. (hist) ‎Sampling Methods ‎[1,814 bytes]
  153. (hist) ‎Ps.m2p ‎[1,823 bytes]
  154. (hist) ‎Rizzo Lab Weekly Group Meetings ‎[1,873 bytes]
  155. (hist) ‎Sequence alignment ‎[1,873 bytes]
  156. (hist) ‎2009 RCR GROUP MEETING ‎[1,878 bytes]
  157. (hist) ‎Announcements: Fall 2013 ‎[1,976 bytes]
  158. (hist) ‎Rsync ‎[1,987 bytes]
  159. (hist) ‎DGHYD ‎[2,002 bytes]
  160. (hist) ‎Unix ‎[2,049 bytes]
  161. (hist) ‎Integration.pl ‎[2,056 bytes]
  162. (hist) ‎AMS-532: Lab Rotations/Journal Club Guidelines ‎[2,065 bytes]
  163. (hist) ‎TIMD integration prep.py ‎[2,100 bytes]
  164. (hist) ‎AMS-532 Guidlines ‎[2,117 bytes]
  165. (hist) ‎Cluster compilations ‎[2,141 bytes]
  166. (hist) ‎Ubq min.mdp ‎[2,155 bytes]
  167. (hist) ‎Stupid awk tricks ‎[2,188 bytes]
  168. (hist) ‎Slick awk tricks ‎[2,188 bytes]
  169. (hist) ‎Families in the Protein Databank ‎[2,247 bytes]
  170. (hist) ‎Make Unique script usage ‎[2,255 bytes]
  171. (hist) ‎MPICH ‎[2,313 bytes]
  172. (hist) ‎Server Administration ‎[2,329 bytes]
  173. (hist) ‎Apply for NYBlue ‎[2,331 bytes]
  174. (hist) ‎MATLAB ‎[2,365 bytes]
  175. (hist) ‎Stony Brook Joint Group Meetings in Computational Structural Biology ‎[2,397 bytes]
  176. (hist) ‎Seawulf Items Needed ‎[2,402 bytes]
  177. (hist) ‎NAMD Amber inputs ‎[2,405 bytes]
  178. (hist) ‎Vi ‎[2,466 bytes]
  179. (hist) ‎Setting up RSA SecureID token ‎[2,470 bytes]
  180. (hist) ‎No t4 step2 equiprod.bash ‎[2,493 bytes]
  181. (hist) ‎With t4 step2 equiprod.bash ‎[2,499 bytes]
  182. (hist) ‎AutoDock4 Benchmark Results ‎[2,506 bytes]
  183. (hist) ‎Joint Group Meeting 2007-2009 ‎[2,541 bytes]
  184. (hist) ‎Formating your Thesis ‎[2,557 bytes]
  185. (hist) ‎Formatting your Thesis ‎[2,557 bytes]
  186. (hist) ‎Run.java.csh ‎[2,566 bytes]
  187. (hist) ‎Installing DOCK ‎[2,577 bytes]
  188. (hist) ‎DOCK Installation ‎[2,577 bytes]
  189. (hist) ‎DOCK GA Development Goals ‎[2,628 bytes]
  190. (hist) ‎2017 RCR GROUP MEETING ‎[2,639 bytes]
  191. (hist) ‎Fragment Library Generation ‎[2,653 bytes]
  192. (hist) ‎DOCK VS Development Goals ‎[2,662 bytes]
  193. (hist) ‎TIMD integration.py ‎[2,731 bytes]
  194. (hist) ‎Scp files from cluster to NYBlue ‎[2,791 bytes]
  195. (hist) ‎Setup ssh tunnel to NYBlue fen ‎[2,802 bytes]
  196. (hist) ‎Rizzo Lab Information and Tutorials ‎[2,860 bytes]
  197. (hist) ‎DOCK DN Parameters ‎[3,028 bytes]
  198. (hist) ‎Parameter List ‎[3,030 bytes]
  199. (hist) ‎No t4 step1 inputgen.bash ‎[3,120 bytes]
  200. (hist) ‎No t4 step3 inputgen.bash ‎[3,126 bytes]
  201. (hist) ‎With t4 step1 inputgen.bash ‎[3,130 bytes]
  202. (hist) ‎With t4 step3 inputgen.bash ‎[3,132 bytes]
  203. (hist) ‎Chimera ‎[3,255 bytes]
  204. (hist) ‎2019-2020 AMS-532 Fall-Spring ‎[3,260 bytes]
  205. (hist) ‎2019 RCR GROUP MEETING ‎[3,400 bytes]
  206. (hist) ‎De novo Benchmarking ‎[3,441 bytes]
  207. (hist) ‎DOCK DN Benchmarking ‎[3,441 bytes]
  208. (hist) ‎04md.in ‎[3,478 bytes]
  209. (hist) ‎Rigid.in ‎[3,481 bytes]
  210. (hist) ‎Apply for cluster ‎[3,485 bytes]
  211. (hist) ‎Other Meetings ‎[3,489 bytes]
  212. (hist) ‎3D Analog Library Generation Using Pubchem and Zinc ‎[3,493 bytes]
  213. (hist) ‎Analog Library - Pubchem & Zinc ‎[3,493 bytes]
  214. (hist) ‎01mi.in ‎[3,552 bytes]
  215. (hist) ‎PBS Queue ‎[3,567 bytes]
  216. (hist) ‎Compiling GROMACS on Cluster ‎[3,789 bytes]
  217. (hist) ‎TIMD extraction.py ‎[3,888 bytes]
  218. (hist) ‎Ubq nvt.mdp ‎[3,999 bytes]
  219. (hist) ‎Automated Families generation from the Protein Databank ‎[4,021 bytes]
  220. (hist) ‎Automated Family generation from PDB ‎[4,021 bytes]
  221. (hist) ‎Ubq md.mdp ‎[4,141 bytes]
  222. (hist) ‎Ubq npt.mdp ‎[4,249 bytes]
  223. (hist) ‎SLURM ‎[4,319 bytes]
  224. (hist) ‎DOCK6 POSE Reproduction ‎[4,323 bytes]
  225. (hist) ‎Flex.in ‎[4,327 bytes]
  226. (hist) ‎2012-2013 AMS-532 Fall-Spring ‎[4,340 bytes]
  227. (hist) ‎RGD ‎[4,424 bytes]
  228. (hist) ‎Virtual Screening SOP ‎[4,498 bytes]
  229. (hist) ‎Restraint04.pdb ‎[4,558 bytes]
  230. (hist) ‎Restraint01.pdb ‎[4,561 bytes]
  231. (hist) ‎GRD-500 Integrity in Science ‎[4,589 bytes]
  232. (hist) ‎CONGA Parameter List ‎[4,724 bytes]
  233. (hist) ‎DOCK GA Parameter List ‎[4,724 bytes]
  234. (hist) ‎2009-2010 AMS-532 Fall-Spring ‎[4,860 bytes]
  235. (hist) ‎DOCK CV Input File(s) ‎[4,925 bytes]
  236. (hist) ‎2018 ‎[5,026 bytes]
  237. (hist) ‎DOCK GA Parameters ‎[5,043 bytes]
  238. (hist) ‎2008-2009 AMS-532 Fall-Spring ‎[5,101 bytes]
  239. (hist) ‎2008 AMS-536 Spring ‎[5,225 bytes]
  240. (hist) ‎2017a DOCK tutorial ‎[5,303 bytes]
  241. (hist) ‎2006-2007 AMS-532 Fall-Spring ‎[5,318 bytes]
  242. (hist) ‎SB2021.v1 ‎[5,385 bytes]
  243. (hist) ‎Activating your Seawulf Account ‎[5,425 bytes]
  244. (hist) ‎2017 Dock tutorial ‎[5,467 bytes]
  245. (hist) ‎2007-2008 AMS-532 Fall-Spring ‎[5,561 bytes]
  246. (hist) ‎Xmgrace ‎[5,581 bytes]
  247. (hist) ‎2009 AMS-536 Spring ‎[5,638 bytes]
  248. (hist) ‎2011 RCR GROUP MEETING ‎[5,659 bytes]
  249. (hist) ‎Rizzo Lab Members and Contact Information ‎[5,702 bytes]
  250. (hist) ‎BOSS Pure Liquid Simulation Notes ‎[5,740 bytes]

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