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Showing below up to 350 results in range #101 to #450.

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  1. 2011 DOCK tutorial with Streptavidin‏‎ (28 revisions)
  2. 2021 Denovo tutorial 3 with PDBID 1S19‏‎ (27 revisions)
  3. 2019 Denovo design tutorial 3 with PDB 3JQZ‏‎ (27 revisions)
  4. Analysis Tools Repository‏‎ (27 revisions)
  5. 2013 AMS-536 Spring‏‎ (27 revisions)
  6. 2014 AMS-536 Spring‏‎ (27 revisions)
  7. 2019 Denovo design tutorial 2 with PDB 2P16‏‎ (26 revisions)
  8. 2019 AMS-535 Fall‏‎ (26 revisions)
  9. 2020 AMS-536 Spring (original syllabus)‏‎ (26 revisions)
  10. 2011 AMS-536 Spring‏‎ (26 revisions)
  11. 2016 AMS-536 Spring‏‎ (26 revisions)
  12. Stony Brook Joint Group Meetings in Computational Structural Biology‏‎ (26 revisions)
  13. 2019 Denovo design tutorial 1 with PDB 2BXF‏‎ (25 revisions)
  14. 2018 Denovo design tutorial 1 with PDB 2NNQ‏‎ (24 revisions)
  15. 2022 Denovo tutorial 2 with PDBID 4ZUD‏‎ (24 revisions)
  16. AMBER Tutorials‏‎ (23 revisions)
  17. 2019 AMBER tutorial with PDBID 2BXF‏‎ (23 revisions)
  18. 2017-2018 AMS-532 Fall-Spring‏‎ (23 revisions)
  19. 2017 AMBER tutorial with 4qmz‏‎ (22 revisions)
  20. 2012 AMS-536 Spring‏‎ (22 revisions)
  21. 2021 AMBER tutorial 1 with PDBID 1HW9‏‎ (22 revisions)
  22. 2018-2019 AMS-532 Fall-Spring‏‎ (22 revisions)
  23. Virtual Screening Protocol‏‎ (21 revisions)
  24. 2020-2021 AMS-532 Fall-Spring‏‎ (21 revisions)
  25. 2020 Denovo tutorial 4 with PDBID 6UZW‏‎ (21 revisions)
  26. NAMD Amber inputs‏‎ (20 revisions)
  27. 2022 AMBER tutorial 1 with PDBID 6ME2‏‎ (20 revisions)
  28. 2017 Dock tutorial‏‎ (20 revisions)
  29. Make Unique script usage‏‎ (20 revisions)
  30. 2019 AMS-536 Spring‏‎ (19 revisions)
  31. DOCK6 POSE Reproduction‏‎ (19 revisions)
  32. Main Page‏‎ (19 revisions)
  33. How to purchase compounds for Rizzo lab‏‎ (19 revisions)
  34. 2022-2023 AMS-532 Fall-Spring‏‎ (18 revisions)
  35. SB2021.v1‏‎ (18 revisions)
  36. Development Goals Archive‏‎ (18 revisions)
  37. Seawulf Items Needed‏‎ (18 revisions)
  38. 2022 Denovo tutorial 3 with PDBID 1X70‏‎ (18 revisions)
  39. 2022 RCR GROUP MEETING‏‎ (17 revisions)
  40. 2014-2015 AMS-532 Fall-Spring‏‎ (17 revisions)
  41. DGHYD‏‎ (16 revisions)
  42. Formating your Thesis‏‎ (16 revisions)
  43. 2016 RCR GROUP MEETING‏‎ (16 revisions)
  44. 2016 AMBER tutorial with Thrombin‏‎ (15 revisions)
  45. DOCK VS Tutorials‏‎ (15 revisions)
  46. 2018 AMS-536 Spring‏‎ (14 revisions)
  47. 2020 Denovo tutorial 1 with PDBID 3VJK‏‎ (14 revisions)
  48. 2021 Denovo tutorial 4 with PDBID 1EFY‏‎ (14 revisions)
  49. Seawulf Cluster Assessment‏‎ (14 revisions)
  50. 2022 Denovo tutorial 1 with PDBID 6ME2‏‎ (14 revisions)
  51. 2020 DOCK tutorial 2 with PDBID 2GQG‏‎ (14 revisions)
  52. 2020 DOCK tutorial 2 with PDBID XXXX‏‎ (14 revisions)
  53. BASH scripting‏‎ (13 revisions)
  54. 2020 Denovo tutorial 3 with PDBID 4F4P‏‎ (13 revisions)
  55. Per-residue energy decompositions‏‎ (13 revisions)
  56. CONGA Parameter List‏‎ (13 revisions)
  57. 2012-2013 AMS-532 Fall-Spring‏‎ (13 revisions)
  58. Energy Scoring Method in Grid‏‎ (13 revisions)
  59. 2018 AMBER tutorial with 1c87‏‎ (13 revisions)
  60. Server Administration‏‎ (12 revisions)
  61. 2018 Denovo design tutorial 2 with PDB 1C87‏‎ (12 revisions)
  62. DOCK Release Objectives‏‎ (12 revisions)
  63. De novo Benchmarking‏‎ (12 revisions)
  64. 2018 RCR GROUP MEETING‏‎ (12 revisions)
  65. 3D Analog Library Generation Using Pubchem and Zinc‏‎ (11 revisions)
  66. Activating your Seawulf Account‏‎ (11 revisions)
  67. Tutorials‏‎ (11 revisions)
  68. 2017 Denovo refine tutorial with PDB 1BJU‏‎ (11 revisions)
  69. Joint Group Meeting 2010‏‎ (11 revisions)
  70. Joint Group Meeting 2011‏‎ (11 revisions)
  71. Nonstandard residues prep‏‎ (11 revisions)
  72. Stupid awk tricks‏‎ (11 revisions)
  73. PBS Queue‏‎ (10 revisions)
  74. Ligand Enrichment Tutorial‏‎ (10 revisions)
  75. 2010 LAB‏‎ (10 revisions)
  76. Compiling GROMACS on Cluster‏‎ (10 revisions)
  77. Apply for cluster‏‎ (10 revisions)
  78. AutoDock Vina Pose Reproduction Tutorial‏‎ (9 revisions)
  79. Chimera‏‎ (9 revisions)
  80. MATLAB‏‎ (9 revisions)
  81. Past Announcements‏‎ (9 revisions)
  82. DOCK Denovo‏‎ (9 revisions)
  83. MPICH‏‎ (9 revisions)
  84. Unix‏‎ (9 revisions)
  85. GRD-500 Integrity in Science‏‎ (9 revisions)
  86. DOCK Denovo Refinement‏‎ (8 revisions)
  87. Small Molecule Evolution (DOCK GA)‏‎ (8 revisions)
  88. AutoDock4 Benchmark Results‏‎ (8 revisions)
  89. DOCK Benchmarking‏‎ (8 revisions)
  90. DOCK CV Benchmarking‏‎ (8 revisions)
  91. Release‏‎ (8 revisions)
  92. DOCK GA Tutorials‏‎ (7 revisions)
  93. 2008 DOCK tutorial with Gleevec‏‎ (7 revisions)
  94. 2022 AMBER tutorial 3 with PDBID 1X70‏‎ (7 revisions)
  95. MD Simulation: Protein in Water (Pt. 2)‏‎ (7 revisions)
  96. MOE‏‎ (7 revisions)
  97. DOCK VS Benchmarking‏‎ (7 revisions)
  98. Fragment Library Generation‏‎ (7 revisions)
  99. 2019 DOCK GA tutorial 1 with 2NNQ‏‎ (7 revisions)
  100. Automated Families generation from the Protein Databank‏‎ (6 revisions)
  101. Legacy Info‏‎ (6 revisions)
  102. 2017 AMS-536 Spring‏‎ (6 revisions)
  103. De Novo Design (DOCK DN)‏‎ (6 revisions)
  104. Example of an Input file‏‎ (6 revisions)
  105. DOCK DN Tutorials‏‎ (6 revisions)
  106. Dell 5110cn Printer‏‎ (6 revisions)
  107. VMD‏‎ (5 revisions)
  108. C Shell Scripting‏‎ (5 revisions)
  109. DOCK GA Parameters‏‎ (5 revisions)
  110. Rsync‏‎ (5 revisions)
  111. Xmgrace‏‎ (5 revisions)
  112. Vi‏‎ (5 revisions)
  113. Cluster compilations‏‎ (5 revisions)
  114. DOCK GIST Parameters‏‎ (5 revisions)
  115. Installing DOCK‏‎ (5 revisions)
  116. 2017 Denovo design tutorial 1 with PDB 1BJU‏‎ (5 revisions)
  117. NOVA (Navigation and Optimization for Virtual Assembly)‏‎ (5 revisions)
  118. Joint Group Meeting 2007-2009‏‎ (5 revisions)
  119. 2009 RCR GROUP MEETING‏‎ (5 revisions)
  120. Scp files from cluster to NYBlue‏‎ (5 revisions)
  121. Joint Group Meeting 2013‏‎ (5 revisions)
  122. 2008-2009 LAB‏‎ (5 revisions)
  123. 2008 AMS-535 Fall‏‎ (5 revisions)
  124. 2008 AMS-536 Spring‏‎ (4 revisions)
  125. DOCK CV Tutorials‏‎ (4 revisions)
  126. Semester Checklist‏‎ (4 revisions)
  127. 2008 RCR GROUP MEETING‏‎ (4 revisions)
  128. LoadLeveler Chain Jobs‏‎ (4 revisions)
  129. SB2011 testset‏‎ (4 revisions)
  130. 2010 RCR GROUP MEETING‏‎ (4 revisions)
  131. 2009-2010 GRD-500 Fall-Spring‏‎ (4 revisions)
  132. SLURM‏‎ (4 revisions)
  133. 2009 DOCK tutorial with neuraminidase‏‎ (4 revisions)
  134. DOCK Abbreviations Guide‏‎ (4 revisions)
  135. HIV/AIDS‏‎ (4 revisions)
  136. DOCK CV Input File(s)‏‎ (3 revisions)
  137. Rotation students Wiki‏‎ (3 revisions)
  138. 2021 Denovo tutorial 2 with PDBID 2ZD1‏‎ (3 revisions)
  139. 2008 DOCK tutorial with 1LAH‏‎ (3 revisions)
  140. Example of an CONGA Input file‏‎ (3 revisions)
  141. General Dock Utilities‏‎ (3 revisions)
  142. Advanced Dock Utilities/Information‏‎ (3 revisions)
  143. 2012 GRD-500 Spring‏‎ (3 revisions)
  144. Setting up RSA SecureID token‏‎ (3 revisions)
  145. Example of an Single Molecule Evolution Input file‏‎ (3 revisions)
  146. Benchmarking‏‎ (3 revisions)
  147. 2009 AMBER tutorial with Trpcage‏‎ (3 revisions)
  148. SDF to mol2‏‎ (3 revisions)
  149. AMS-532 Guidlines‏‎ (3 revisions)
  150. BlueGene‏‎ (3 revisions)
  151. Joint Group Meeting 2012‏‎ (3 revisions)
  152. RGD‏‎ (3 revisions)
  153. Fourier fit‏‎ (3 revisions)
  154. R - Statistical Computing‏‎ (3 revisions)
  155. Unix find‏‎ (3 revisions)
  156. 2018‏‎ (3 revisions)
  157. 2008 AMBER tutorial‏‎ (3 revisions)
  158. AutoDock Vina Benchmark Results‏‎ (3 revisions)
  159. Ethernet Cables‏‎ (2 revisions)
  160. Gdb (GNU Debugger)‏‎ (2 revisions)
  161. Method development‏‎ (2 revisions)
  162. Sed - Stream Editor in Unix‏‎ (2 revisions)
  163. Valgrind‏‎ (2 revisions)
  164. DOCK Compilation‏‎ (2 revisions)
  165. De Novo Design‏‎ (2 revisions)
  166. Example of an Ensemble Evolution Input file‏‎ (2 revisions)
  167. NAMD on Seawulf‏‎ (2 revisions)
  168. Parameter List/Explanations‏‎ (2 revisions)
  169. Genion.mdp‏‎ (2 revisions)
  170. Testset Protocols‏‎ (2 revisions)
  171. Amber to mol2 (protein)‏‎ (2 revisions)
  172. ZINC Database‏‎ (2 revisions)
  173. Get Job ids to use for llcancel‏‎ (2 revisions)
  174. DOCK DN Parameters‏‎ (2 revisions)
  175. Virtual Screening SOP‏‎ (2 revisions)
  176. No t4 step1 inputgen.bash‏‎ (2 revisions)
  177. Ps.m2p‏‎ (2 revisions)
  178. Ubq min.mdp‏‎ (2 revisions)
  179. DOCK DN Utilities‏‎ (2 revisions)
  180. Getting a BNL Account‏‎ (2 revisions)
  181. AMS-532: Lab Rotations/Journal Club Guidelines‏‎ (2 revisions)
  182. Ubq npt.mdp‏‎ (2 revisions)
  183. 2009 AMS-536 Spring‏‎ (2 revisions)
  184. Footprint Plot Visualization‏‎ (2 revisions)
  185. 2017 Denovo refinement tutorial with PDB 1BJU‏‎ (2 revisions)
  186. Ubq nvt.mdp‏‎ (2 revisions)
  187. Developer's Info‏‎ (2 revisions)
  188. Pylab‏‎ (2 revisions)
  189. CONGA‏‎ (2 revisions)
  190. 2011 GRD-500 Spring‏‎ (2 revisions)
  191. 2017a DOCK tutorial‏‎ (2 revisions)
  192. Sphere Generation‏‎ (2 revisions)
  193. 2010-2011 GRD-500 Fall-Spring‏‎ (2 revisions)
  194. CVS Commands‏‎ (2 revisions)
  195. DOCK CV Development Goals‏‎ (2 revisions)
  196. Making images for publication using vmd‏‎ (2 revisions)
  197. Outdated Info‏‎ (1 revisions)
  198. Remove waters from trajectories‏‎ (1 revisions)
  199. Robert C. Rizzo Research Group‏‎ (1 revisions - redirect page)
  200. Secure Shell (ssh)‏‎ (1 revisions)
  201. Submitting BleuGene Jobs‏‎ (1 revisions - redirect page)
  202. AMS 532: Lab Rotations/Journal Club Guidelines‏‎ (1 revisions - redirect page)
  203. With t4 step3 inputgen.bash‏‎ (1 revisions)
  204. DOCK GA Parameter List‏‎ (1 revisions)
  205. DOCK tutorial with 1LAH‏‎ (1 revisions - redirect page)
  206. INSPH‏‎ (1 revisions)
  207. Lab-specific Tutorials‏‎ (1 revisions - redirect page)
  208. Rename files in Unix‏‎ (1 revisions)
  209. Submitting BlueGene Jobs‏‎ (1 revisions)
  210. VMD tutorial‏‎ (1 revisions - redirect page)
  211. X-Win32‏‎ (1 revisions)
  212. Cancer‏‎ (1 revisions)
  213. DOCK tutorial with Gleevec‏‎ (1 revisions - redirect page)
  214. Example Input Files‏‎ (1 revisions)
  215. General Dock Development Goals‏‎ (1 revisions)
  216. Influenza‏‎ (1 revisions)
  217. Min.mdp‏‎ (1 revisions - redirect page)
  218. PDFCreator‏‎ (1 revisions)
  219. Research Foundation‏‎ (1 revisions)
  220. 2020 DOCK tutorial 4 with PDBID XXXX‏‎ (1 revisions)
  221. AMBER Lipid Tutorials‏‎ (1 revisions)
  222. TIMD extraction.py‏‎ (1 revisions)
  223. Advanced Dock Utilities‏‎ (1 revisions)
  224. Automated Family generation from PDB‏‎ (1 revisions)
  225. DOCK tutorial with neuraminidase‏‎ (1 revisions - redirect page)
  226. Input for md‏‎ (1 revisions - redirect page)
  227. Restraint.vmd.script‏‎ (1 revisions)
  228. Run.java.csh‏‎ (1 revisions)
  229. Sequence alignment‏‎ (1 revisions)
  230. TIMD integration.py‏‎ (1 revisions)
  231. ZINC12 Database‏‎ (1 revisions)
  232. DOCK DN Benchmarking‏‎ (1 revisions)
  233. 2010 GRD-500 Spring‏‎ (1 revisions)
  234. General Dock Utilities/Info‏‎ (1 revisions)
  235. Input for min‏‎ (1 revisions - redirect page)
  236. Restraint01.pdb‏‎ (1 revisions)
  237. 2020 Denovo tutorial 2 with PDBID 2GQG‏‎ (1 revisions)
  238. TIMD integration prep.py‏‎ (1 revisions)
  239. Vi tutorial‏‎ (1 revisions - redirect page)
  240. BOSS Pure Liquid Simulation‏‎ (1 revisions - redirect page)
  241. Clustering in R‏‎ (1 revisions)
  242. DOCK Installation‏‎ (1 revisions)
  243. 01mi.in‏‎ (1 revisions)
  244. 2008 Spring‏‎ (1 revisions)
  245. NAMD to mol2‏‎ (1 revisions)
  246. NAMD tutorial‏‎ (1 revisions)
  247. Restraint04.pdb‏‎ (1 revisions)
  248. AMBER tricks‏‎ (1 revisions)
  249. BOSS Pure Liquid Simulation Notes‏‎ (1 revisions)
  250. Coming Soon‏‎ (1 revisions)
  251. DOCK DN Input File(s)‏‎ (1 revisions)
  252. DOCK NOVA‏‎ (1 revisions)
  253. 04md.in‏‎ (1 revisions)
  254. De Novo Design (previously NOVA)‏‎ (1 revisions)
  255. Installing MSMS for VMD‏‎ (1 revisions)
  256. NOVA‏‎ (1 revisions)
  257. Pdb to mol2‏‎ (1 revisions)
  258. Rigid.in‏‎ (1 revisions)
  259. Setting up insurance through Research Foundation‏‎ (1 revisions)
  260. AMBER tutorial‏‎ (1 revisions - redirect page)
  261. Amber to pdb‏‎ (1 revisions)
  262. BOSS pure liquid simulation‏‎ (1 revisions - redirect page)
  263. Common Errors - ctrl M‏‎ (1 revisions)
  264. 2006-2007 AMS-532 Fall-Spring‏‎ (1 revisions)
  265. Example scripts‏‎ (1 revisions)
  266. Get time estimate for free blocks‏‎ (1 revisions)
  267. Integration.pl‏‎ (1 revisions)
  268. Rizzo Lab-specific Information and Tutorials‏‎ (1 revisions - redirect page)
  269. Setup ssh tunnel to NYBlue fen‏‎ (1 revisions)
  270. AMBER tutorial with Trpcage‏‎ (1 revisions - redirect page)
  271. Ubq md.mdp‏‎ (1 revisions)
  272. Analog Library - Pubchem & Zinc‏‎ (1 revisions)
  273. Compiling Applications for BG/L‏‎ (1 revisions)
  274. DOCK Tutorial with 1LAH‏‎ (1 revisions - redirect page)
  275. 2007-2006 AMS-532 Fall-Spring‏‎ (1 revisions - redirect page)
  276. De novo DOCK‏‎ (1 revisions)
  277. Families in the Protein Databank‏‎ (1 revisions)
  278. 2011-2012 GRD-500 Fall-Spring‏‎ (1 revisions)
  279. Get time for job completion‏‎ (1 revisions)
  280. MD of Protein in Water‏‎ (1 revisions - redirect page)
  281. 2017 Denovo design tutorial with PDB 1BJU‏‎ (1 revisions)
  282. Rizzo Lab Contact Information‏‎ (1 revisions - redirect page)
  283. Showbox.in‏‎ (1 revisions)
  284. Visiting BNL‏‎ (1 revisions)
  285. Binding Footprint Program‏‎ (1 revisions)
  286. 2007-2008 AMS-532 Fall-Spring‏‎ (1 revisions)
  287. Flex.in‏‎ (1 revisions)
  288. No t4 step2 equiprod.bash‏‎ (1 revisions)
  289. Ptraj‏‎ (1 revisions)
  290. 2022 Covalent docking tutorial updated with PDB xxxx‏‎ (1 revisions)
  291. Showsph.in‏‎ (1 revisions)
  292. Announcements: Fall 2013‏‎ (1 revisions)
  293. Vmd.rmsd.csh‏‎ (1 revisions)
  294. Blocked Standard Error of the Mean‏‎ (1 revisions)
  295. Config‏‎ (1 revisions)
  296. DOCK DN Utilities/Info‏‎ (1 revisions)
  297. 2007-2009‏‎ (1 revisions - redirect page)
  298. Ghostscript‏‎ (1 revisions)
  299. MOE Tutorial‏‎ (1 revisions - redirect page)
  300. No t4 step2 min.bash‏‎ (1 revisions)
  301. Pure Liquid Simulation‏‎ (1 revisions - redirect page)
  302. Sampling Methods‏‎ (1 revisions)
  303. Simple Protein in Water MD‏‎ (1 revisions - redirect page)
  304. Apply for NYBlue‏‎ (1 revisions)
  305. Ways to remove the first line‏‎ (1 revisions)
  306. 2008-2007 AMS-532 Fall-Spring‏‎ (1 revisions - redirect page)
  307. Gnuplot‏‎ (1 revisions)
  308. No t4 step3 inputgen.bash‏‎ (1 revisions)
  309. Slick awk tricks‏‎ (1 revisions)
  310. Which Unix Distribution?‏‎ (1 revisions)
  311. BlueGene LoadLeveler Jobs with Multiple Steps (Chain Jobs)‏‎ (1 revisions - redirect page)
  312. DOCK VS Parameters‏‎ (1 revisions)
  313. 2008-2009‏‎ (1 revisions - redirect page)
  314. Formatting your Thesis‏‎ (1 revisions)
  315. Grid.in‏‎ (1 revisions)
  316. Unix Tutorial‏‎ (1 revisions - redirect page)
  317. Archiving old data‏‎ (1 revisions)
  318. Wiki Editing‏‎ (1 revisions)
  319. 2008-2009 AMS-532 Fall-Spring‏‎ (1 revisions)
  320. 2010‏‎ (1 revisions - redirect page)
  321. Octave‏‎ (1 revisions)
  322. 2020 DOCK tutorial 1 with PDBID XXXX‏‎ (1 revisions)
  323. AMS-532 Laboratory Rotations and Journal Club in Computational Structural Biology‏‎ (1 revisions - redirect page)
  324. With t4 step1 inputgen.bash‏‎ (1 revisions)
  325. CONGA (CONstruction by Genetic Algorithm)‏‎ (1 revisions)
  326. DOCK GA Developer Progress‏‎ (1 revisions)
  327. DOCK VS Utilities‏‎ (1 revisions)
  328. Disulfide.txt‏‎ (1 revisions)
  329. Hello World‏‎ (1 revisions - redirect page)
  330. Journal Articles from UCSF‏‎ (1 revisions)
  331. 2016 DOCK tutorial with Thrombin‏‎ (1 revisions - redirect page)
  332. Make surface‏‎ (1 revisions)
  333. Optimize Polar Hydrogens‏‎ (1 revisions)
  334. Reference.vmd.script‏‎ (1 revisions)
  335. Using Small Ligands with AMBER, complete tutorial‏‎ (1 revisions - redirect page)
  336. With t4 step2 equiprod.bash‏‎ (1 revisions)
  337. DOCK VS Utilities/Info‏‎ (1 revisions)
  338. Drug-like organic molecules‏‎ (1 revisions)
  339. Free Energy of Hydration Test-set‏‎ (1 revisions - redirect page)
  340. Histograms in R‏‎ (1 revisions)
  341. Lab-designed code and programs‏‎ (1 revisions)
  342. Making images for publication‏‎ (1 revisions)
  343. Other Meetings‏‎ (1 revisions)
  344. Rizzo Lab Wiki‏‎ (1 revisions - redirect page)
  345. Seawulf Programs Needed‏‎ (1 revisions)
  346. Using convert command unix‏‎ (1 revisions)
  347. With t4 step2 min.bash‏‎ (1 revisions)
  348. DOCK GA Input File(s)‏‎ (1 revisions)
  349. DOCK tutorial‏‎ (1 revisions - redirect page)
  350. Lab-specific Information and Tutorials‏‎ (1 revisions - redirect page)

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