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  1. 01mi.in
  2. 04md.in
  3. 2006-2007 AMS-532 Fall-Spring
  4. 2007-2008 AMS-532 Fall-Spring
  5. 2008-2009 AMS-532 Fall-Spring
  6. 2008-2009 LAB
  7. 2008 AMS-535 Fall
  8. 2008 AMS-536 Spring
  9. 2008 RCR GROUP MEETING
  10. 2008 Spring
  11. 2009-2010 AMS-532 Fall-Spring
  12. 2009-2010 GRD-500 Fall-Spring
  13. 2009 AMS-536 Spring
  14. 2009 RCR GROUP MEETING
  15. 2010-2011 AMS-532 Fall-Spring
  16. 2010-2011 GRD-500 Fall-Spring
  17. 2010 AMS-536 Spring
  18. 2010 GRD-500 Spring
  19. 2010 LAB
  20. 2010 RCR GROUP MEETING
  21. 2011-2012 AMS-532 Fall-Spring
  22. 2011-2012 GRD-500 Fall-Spring
  23. 2011 AMS-535 Fall
  24. 2011 AMS-536 Spring
  25. 2011 GRD-500 Spring
  26. 2011 RCR GROUP MEETING
  27. 2012-2013 AMS-532 Fall-Spring
  28. 2012 AMS-535 Fall
  29. 2012 GRD-500 Spring
  30. 2012 RCR GROUP MEETING
  31. 2013-2014 AMS-532 Fall-Spring
  32. 2013 RCR GROUP MEETING
  33. 2014-2015 AMS-532 Fall-Spring
  34. 2014 AMS-535 Fall
  35. 2014 RCR GROUP MEETING
  36. 2015-2016 AMS-532 Fall-Spring
  37. 2015 AMS-535 Fall
  38. 2015 RCR GROUP MEETING
  39. 2016-2017 AMS-532 Fall-Spring
  40. 2016 AMS-535 Fall
  41. 2016 RCR GROUP MEETING
  42. 2017-2018 AMS-532 Fall-Spring
  43. 2017 AMBER tutorial with 4qmz
  44. 2017 AMS-535 Fall
  45. 2017 Denovo design tutorial 1 with PDB 1BJU
  46. 2017 Denovo design tutorial 2 with PDB 4QMZ
  47. 2017 Denovo design tutorial with PDB 1BJU
  48. 2017 Denovo refinement tutorial with PDB 1BJU
  49. 2017 RCR GROUP MEETING
  50. 2018
  51. 2018-2019 AMS-532 Fall-Spring
  52. 2018 AMBER tutorial with 1c87
  53. 2018 AMBER tutorial with 2nnq
  54. 2018 AMS-535 Fall
  55. 2018 DOCK tutorial 1 with PDBID 2NNQ
  56. 2018 Denovo design tutorial 1 with PDB 2NNQ
  57. 2018 Denovo design tutorial 2 with PDB 1C87
  58. 2018 RCR GROUP MEETING
  59. 2019-2020 AMS-532 Fall-Spring
  60. 2019 AMBER tutorial with PDBID 2BXF
  61. 2019 AMS-535 Fall
  62. 2019 Covalent docking tutorial 1 with PDB 2VKG
  63. 2019 Covalent docking tutorial 1 with PDB 5VKG
  64. 2019 DOCK GA tutorial 1 with 2NNQ
  65. 2019 DOCK tutorial 1 with PDBID 2BXF
  66. 2019 DOCK tutorial 2 with PDBID 2P16
  67. 2019 DOCK tutorial 3 with PDBID 3JQZ
  68. 2019 Denovo design tutorial 1 with PDB 2BXF
  69. 2019 Denovo design tutorial 2 with PDB 2P16
  70. 2019 RCR GROUP MEETING
  71. 2020-2021 AMS-532 Fall-Spring
  72. 2020 AMBER tutorial with PDBID 3VJK
  73. 2020 AMS-535 Fall
  74. 2020 DOCK tutorial 1 with PDBID 3VJK
  75. 2020 DOCK tutorial 1 with PDBID XXXX
  76. 2020 DOCK tutorial 2 with PDBID 2GQG
  77. 2020 DOCK tutorial 2 with PDBID XXXX
  78. 2020 DOCK tutorial 3 with PDBID 4F4P
  79. 2020 DOCK tutorial 4 with PDBID 6UZW
  80. 2020 DOCK tutorial 4 with PDBID XXXX
  81. 2020 Denovo tutorial 1 with PDBID 3VJK
  82. 2020 Denovo tutorial 2 with PDBID 2GQG
  83. 2020 Denovo tutorial 3 with PDBID 4F4P
  84. 2020 Denovo tutorial 4 with PDBID 6UZW
  85. 2021 DOCK tutorial 1 with PDBID 1HW9
  86. 2021 DOCK tutorial 3 with PDBID 1S19
  87. 3D Analog Library Generation Using Pubchem and Zinc
  88. AMBER Lipid Tutorials
  89. AMS-531 Laboratory Rotations in Computational Biology
  90. AMS-532: Lab Rotations/Journal Club Guidelines
  91. AMS-532 Guidlines
  92. Activating your Seawulf Account
  93. Amber on Seawulf (compilation)
  94. Amber to mol2 (protein)
  95. Amber to pdb
  96. Analog Library - Pubchem & Zinc
  97. Analysis Tools Repository
  98. Announcements: Fall 2013
  99. Apply for cluster
  100. Archiving old data
  101. AutoDock4 Benchmark Results
  102. AutoDock4 Pose Reproduction Tutorial
  103. AutoDock Vina Benchmark Results
  104. AutoDock Vina Pose Reproduction Tutorial
  105. Automated Families generation from the Protein Databank
  106. Automated Family generation from PDB
  107. BOSS Pure Liquid Simulation Notes
  108. Blocked Standard Error of the Mean
  109. CONGA Parameter List
  110. CVS Commands
  111. C Shell Scripting
  112. Cancer
  113. Chimera
  114. Cluster compilations
  115. Clustering in R
  116. Coming Soon
  117. Common Errors - ctrl M
  118. Compiling Applications for BG/L
  119. Compiling GROMACS on Cluster
  120. Config
  121. DOCK6 POSE Reproduction
  122. DOCK Abbreviations Guide
  123. DOCK Benchmarking
  124. DOCK CV Benchmarking
  125. DOCK CV Development Goals
  126. DOCK CV Input File(s)
  127. DOCK Compilation
  128. DOCK DN Benchmarking
  129. DOCK DN Development Goals
  130. DOCK DN Input File(s)
  131. DOCK DN Parameters
  132. DOCK Denovo Refinement
  133. DOCK Denovo Run
  134. DOCK GA Developer Progress
  135. DOCK GA Development Goals
  136. DOCK GA Parameter List
  137. DOCK GA Parameters
  138. DOCK GIST Parameters
  139. DOCK Installation
  140. DOCK Release Objectives
  141. DOCK VS Benchmarking
  142. DOCK VS Development Goals
  143. De Novo Design
  144. De novo Benchmarking
  145. De novo Developer Progress
  146. Dell 5110cn Printer
  147. Disulfide.txt
  148. Drug-like organic molecules
  149. Energy Scoring Method in Grid
  150. Ethernet Cables
  151. Example of an CONGA Input file
  152. Example of an Ensemble Evolution Input file
  153. Example of an Input file
  154. Example of an Single Molecule Evolution Input file
  155. Example scripts
  156. Families in the Protein Databank
  157. Flex.in
  158. Footprint Plot Visualization
  159. Fourier fit
  160. Fragment Library Generation
  161. Gdb (GNU Debugger)
  162. General Dock Development Goals
  163. Genion.mdp
  164. Get Job ids to use for llcancel
  165. Get time estimate for free blocks
  166. Get time for job completion
  167. Ghostscript
  168. Grid.in
  169. HIV/AIDS
  170. Histograms in R
  171. How to purchase compounds for Rizzo lab
  172. INSPH
  173. Influenza
  174. Installing DOCK
  175. Installing MSMS for VMD
  176. Integration.pl
  177. Joe and Brian de novo stuff
  178. Joint Group Meeting 2007-2009
  179. Joint Group Meeting 2010
  180. Journal Articles from UCSF
  181. Ligand Enrichment Tutorial
  182. LoadLeveler Chain Jobs
  183. MOE
  184. MPICH
  185. Make Unique script usage
  186. Make surface
  187. Making images for publication using vmd
  188. Method development
  189. NAMD Amber inputs
  190. NAMD to mol2
  191. No t4 step1 inputgen.bash
  192. No t4 step2 equiprod.bash
  193. No t4 step2 min.bash
  194. No t4 step3 inputgen.bash
  195. Nonstandard residues prep
  196. Octave
  197. Optimize Polar Hydrogens
  198. Other Meetings
  199. PDFCreator
  200. Parameter List
  201. Past Announcements
  202. Pdb to mol2
  203. Per-residue energy decompositions
  204. Ps.m2p
  205. Ptraj
  206. Pylab
  207. RGD
  208. Reference.vmd.script
  209. Release
  210. Remove waters from trajectories
  211. Rename files in Unix
  212. Research Foundation
  213. Restraint.vmd.script
  214. Restraint01.pdb
  215. Restraint04.pdb
  216. Rigid.in
  217. Rizzo Lab Members and Contact Information
  218. Rizzo Lab Publications
  219. Rizzo Lab Research
  220. Rotation students Wiki
  221. Rsync
  222. Run.java.csh
  223. SB2011 testset
  224. SDF to mol2
  225. SLURM
  226. Sampling Methods
  227. Scoring Functions
  228. Seawulf Cluster Assessment
  229. Seawulf Items Needed
  230. Seawulf Programs Needed
  231. Secure Shell (ssh)
  232. Sed - Stream Editor in Unix
  233. Semester Checklist
  234. Sequence alignment
  235. Server Administration
  236. Setting up RSA SecureID token
  237. Setting up insurance through Research Foundation
  238. Setup ssh tunnel to NYBlue fen
  239. Showbox.in
  240. Showsph.in
  241. Slick awk tricks
  242. Sphere Generation
  243. Stupid awk tricks
  244. Submitting BlueGene Jobs
  245. TIMD extraction.py
  246. TIMD integration.py
  247. TIMD integration prep.py
  248. Ubq md.mdp
  249. Ubq min.mdp
  250. Ubq npt.mdp
  251. Ubq nvt.mdp
  252. Unix
  253. Unix find
  254. Using convert command unix
  255. Valgrind
  256. Vi
  257. Virtual Screening Protocol
  258. Virtual Screening Protocol on BlueGene (IGF-IR system)
  259. Visiting BNL
  260. Vmd.rmsd.csh
  261. Ways to remove the first line
  262. Which Unix Distribution?
  263. Wiki Editing
  264. With t4 step1 inputgen.bash
  265. With t4 step2 equiprod.bash
  266. With t4 step2 min.bash
  267. With t4 step3 inputgen.bash
  268. X-Win32
  269. Xmgrace
  270. ZINC12 Database
  271. ZINC15 Database
  272. ZINC Database

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