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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 AMBER tutorial
  8. 2008 AMS-535 Fall
  9. 2008 AMS-536 Spring
  10. 2008 DOCK tutorial with 1LAH
  11. 2008 DOCK tutorial with Gleevec
  12. 2008 RCR GROUP MEETING
  13. 2008 Spring
  14. 2009-2010 AMS-532 Fall-Spring
  15. 2009-2010 GRD-500 Fall-Spring
  16. 2009 AMBER tutorial with Trpcage
  17. 2009 AMS-535 Fall
  18. 2009 AMS-536 Spring
  19. 2009 DOCK tutorial with neuraminidase
  20. 2009 RCR GROUP MEETING
  21. 2010-2011 AMS-532 Fall-Spring
  22. 2010-2011 GRD-500 Fall-Spring
  23. 2010 AMBER Tutorial with Biotin and Streptavidin
  24. 2010 AMS-535 Fall
  25. 2010 AMS-536 Spring
  26. 2010 DOCK tutorial with Streptavidin
  27. 2010 GRD-500 Spring
  28. 2010 LAB
  29. 2010 RCR GROUP MEETING
  30. 2011-2012 AMS-532 Fall-Spring
  31. 2011-2012 GRD-500 Fall-Spring
  32. 2011 AMBER Tutorial with Biotin and Streptavidin
  33. 2011 AMS-535 Fall
  34. 2011 AMS-536 Spring
  35. 2011 DOCK tutorial with Streptavidin
  36. 2011 GRD-500 Spring
  37. 2011 RCR GROUP MEETING
  38. 2012-2013 AMS-532 Fall-Spring
  39. 2012 AMBER Tutorial with Biotin and Streptavidin
  40. 2012 AMS-535 Fall
  41. 2012 AMS-536 Spring
  42. 2012 DOCK tutorial with Streptavidin
  43. 2012 GRD-500 Spring
  44. 2012 RCR GROUP MEETING
  45. 2013-2014 AMS-532 Fall-Spring
  46. 2013 AMBER Tutorial with UMP and OMP
  47. 2013 AMS-535 Fall
  48. 2013 AMS-536 Spring
  49. 2013 DOCK tutorial with Orotodine Monophosphate Decarboxylase
  50. 2013 RCR GROUP MEETING
  51. 2014-2015 AMS-532 Fall-Spring
  52. 2014 AMBER tutorial with HIV Protease
  53. 2014 AMS-535 Fall
  54. 2014 AMS-536 Spring
  55. 2014 DOCK tutorial with HIV Protease
  56. 2014 RCR GROUP MEETING
  57. 2015-2016 AMS-532 Fall-Spring
  58. 2015 AMBER tutorial with PARP
  59. 2015 AMS-535 Fall
  60. 2015 AMS-536 Spring
  61. 2015 DOCK tutorial with Poly(ADP-ribose) polymerase (PARP)
  62. 2015 RCR GROUP MEETING
  63. 2016-2017 AMS-532 Fall-Spring
  64. 2016 AMBER tutorial with Beta Trypsin
  65. 2016 AMBER tutorial with Thrombin
  66. 2016 AMS-535 Fall
  67. 2016 AMS-536 Spring
  68. 2016 DOCK tutorial with Beta Trypsin
  69. 2016 RCR GROUP MEETING
  70. 2017-2018 AMS-532 Fall-Spring
  71. 2017 AMBER tutorial with 4qmz
  72. 2017 AMS-535 Fall
  73. 2017 AMS-536 Spring
  74. 2017 DOCK tutorial 1 with PDB 4QMZ NEW
  75. 2017 DOCK tutorial 2 with PDB 3GPL NEW
  76. 2017 Denovo design tutorial 1 with PDB 1BJU
  77. 2017 Denovo design tutorial 2 with PDB 4QMZ
  78. 2017 Denovo design tutorial with PDB 1BJU
  79. 2017 Denovo refine tutorial with PDB 1BJU
  80. 2017 Denovo refinement tutorial with PDB 1BJU
  81. 2017 Dock tutorial
  82. 2017 RCR GROUP MEETING
  83. 2017a DOCK tutorial
  84. 2018
  85. 2018-2019 AMS-532 Fall-Spring
  86. 2018 AMBER tutorial with 1c87
  87. 2018 AMBER tutorial with 2nnq
  88. 2018 AMS-535 Fall
  89. 2018 AMS-536 Spring
  90. 2018 DOCK tutorial 1 with PDBID 2NNQ
  91. 2018 DOCK tutorial 2 with PDBID 1C87
  92. 2018 Denovo design tutorial 1 with PDB 2NNQ
  93. 2018 Denovo design tutorial 2 with PDB 1C87
  94. 2018 RCR GROUP MEETING
  95. 2019-2020 AMS-532 Fall-Spring
  96. 2019 AMBER tutorial with PDBID 2BXF
  97. 2019 AMS-535 Fall
  98. 2019 AMS-536 Spring
  99. 2019 Covalent docking tutorial 1 with PDB 2VKG
  100. 2019 Covalent docking tutorial 1 with PDB 5VKG
  101. 2019 DOCK GA tutorial 1 with 2NNQ
  102. 2019 DOCK tutorial 1 with PDBID 2BXF
  103. 2019 DOCK tutorial 2 with PDBID 2P16
  104. 2019 DOCK tutorial 3 with PDBID 3JQZ
  105. 2019 Denovo design tutorial 1 with PDB 2BXF
  106. 2019 Denovo design tutorial 2 with PDB 2P16
  107. 2019 Denovo design tutorial 3 with PDB 3JQZ
  108. 2019 RCR GROUP MEETING
  109. 2020-2021 AMS-532 Fall-Spring
  110. 2020 AMBER tutorial with PDBID 3VJK
  111. 2020 AMS-535 Fall
  112. 2020 AMS-536 Spring
  113. 2020 AMS-536 Spring (original syllabus)
  114. 2020 AMS-536 Spring (revised syllabus)
  115. 2020 DOCK tutorial 1 with PDBID 3VJK
  116. 2020 DOCK tutorial 1 with PDBID XXXX
  117. 2020 DOCK tutorial 2 with PDBID 2GQG
  118. 2020 DOCK tutorial 2 with PDBID XXXX
  119. 2020 DOCK tutorial 3 with PDBID 4F4P
  120. 2020 DOCK tutorial 4 with PDBID 6UZW
  121. 2020 DOCK tutorial 4 with PDBID XXXX
  122. 2020 Denovo tutorial 1 with PDBID 3VJK
  123. 2020 Denovo tutorial 2 with PDBID 2GQG
  124. 2020 Denovo tutorial 3 with PDBID 4F4P
  125. 2020 Denovo tutorial 4 with PDBID 6UZW
  126. 2021-2022 AMS-532 Fall-Spring
  127. 2021 AMBER tutorial 1 with PDBID 1HW9
  128. 2021 AMBER tutorial 3 with PDBID 1S19
  129. 2021 AMS-535 Fall
  130. 2021 AMS-536 Spring
  131. 2021 DOCK tutorial 1 with PDBID 1HW9
  132. 2021 DOCK tutorial 2 with PDBID 2ZD1
  133. 2021 DOCK tutorial 3 with PDBID 1S19
  134. 2021 DOCK tutorial 4 with PDBID 1EFY
  135. 2021 Denovo tutorial 1 with PDBID 1HW9
  136. 2021 Denovo tutorial 2 with PDBID 2ZD1
  137. 2021 Denovo tutorial 3 with PDBID 1S19
  138. 2021 Denovo tutorial 4 with PDBID 1EFY
  139. 2022 AMS-536 Spring
  140. 3D Analog Library Generation Using Pubchem and Zinc
  141. AMBER Lipid Tutorials
  142. AMBER TI Tutorials
  143. AMBER Tutorials
  144. AMBER tricks
  145. AMS-531 Laboratory Rotations in Computational Biology
  146. AMS-532: Lab Rotations/Journal Club Guidelines
  147. AMS-532 Guidlines
  148. AMS-532 Journal Club in Computational Biology
  149. AMS-532 Laboratory Rotations and Journal Club in Computational Biology
  150. AMS-535 Introduction to Computational Structural Biology and Drug Design
  151. AMS-536 Molecular Modeling of Biological Molecules
  152. Activating your Seawulf Account
  153. Advanced Dock Utilities
  154. Advanced Dock Utilities/Information
  155. Amber on Seawulf (compilation)
  156. Amber to mol2 (protein)
  157. Amber to pdb
  158. Analog Library - Pubchem & Zinc
  159. Analysis Tools Repository
  160. Announcements: Fall 2013
  161. Apply for NYBlue
  162. Apply for cluster
  163. Archiving old data
  164. AutoDock4 Benchmark Results
  165. AutoDock4 Pose Reproduction Tutorial
  166. AutoDock Vina Benchmark Results
  167. AutoDock Vina Pose Reproduction Tutorial
  168. Automated Families generation from the Protein Databank
  169. Automated Family generation from PDB
  170. BASH scripting
  171. BOSS Pure Liquid Simulation Notes
  172. Benchmarking
  173. Binding Footprint Program
  174. Blocked Standard Error of the Mean
  175. BlueGene
  176. CONGA
  177. CONGA (CONstruction by Genetic Algorithm)
  178. CONGA Parameter List
  179. CVS Commands
  180. C Shell Scripting
  181. Cancer
  182. Chimera
  183. Cluster compilations
  184. Clustering in R
  185. Coming Soon
  186. Common Errors - ctrl M
  187. Compiling Applications for BG/L
  188. Compiling GROMACS on Cluster
  189. Config
  190. DGHYD
  191. DOCK6 POSE Reproduction
  192. DOCK Abbreviations Guide
  193. DOCK Benchmarking
  194. DOCK CV Benchmarking
  195. DOCK CV Development Goals
  196. DOCK CV Input File(s)
  197. DOCK CV Tutorials
  198. DOCK Compilation
  199. DOCK DN Benchmarking
  200. DOCK DN Development Goals
  201. DOCK DN Input File(s)
  202. DOCK DN Parameters
  203. DOCK DN Tutorials
  204. DOCK DN Utilities
  205. DOCK DN Utilities/Info
  206. DOCK Denovo
  207. DOCK Denovo Refinement
  208. DOCK Denovo Run
  209. DOCK GA Developer Progress
  210. DOCK GA Development Goals
  211. DOCK GA Input File(s)
  212. DOCK GA Parameter List
  213. DOCK GA Parameters
  214. DOCK GA Tutorials
  215. DOCK GIST Parameters
  216. DOCK Installation
  217. DOCK NOVA
  218. DOCK Release Objectives
  219. DOCK Tutorials
  220. DOCK VS Benchmarking
  221. DOCK VS Development Goals
  222. DOCK VS Parameters
  223. DOCK VS Tutorials
  224. DOCK VS Utilities
  225. DOCK VS Utilities/Info
  226. De Novo Design
  227. De Novo Design (DOCK DN)
  228. De Novo Design (previously NOVA)
  229. De novo Benchmarking
  230. De novo DOCK
  231. De novo Developer Progress
  232. Dell 5110cn Printer
  233. Developer's Info
  234. Disulfide.txt
  235. Drug-like organic molecules
  236. Energy Scoring Method in Grid
  237. Ethernet Cables
  238. Example Input Files
  239. Example of an CONGA Input file
  240. Example of an Ensemble Evolution Input file
  241. Example of an Input file
  242. Example of an Single Molecule Evolution Input file
  243. Example scripts
  244. Families in the Protein Databank
  245. Flex.in
  246. Footprint Plot Visualization
  247. Formating your Thesis
  248. Formatting your Thesis
  249. Fourier fit
  250. Fragment Library Generation
  251. GRD-500 Integrity in Science
  252. Gdb (GNU Debugger)
  253. General Dock Development Goals
  254. General Dock Utilities
  255. General Dock Utilities/Info
  256. Genion.mdp
  257. Get Job ids to use for llcancel
  258. Get time estimate for free blocks
  259. Get time for job completion
  260. Getting a BNL Account
  261. Ghostscript
  262. Gnuplot
  263. Grid.in
  264. HIV/AIDS
  265. Histograms in R
  266. How to purchase compounds for Rizzo lab
  267. INSPH
  268. Influenza
  269. Installing DOCK
  270. Installing MSMS for VMD
  271. Integration.pl
  272. Joe and Brian de novo stuff
  273. Joint Group Meeting 2007-2009
  274. Joint Group Meeting 2010
  275. Joint Group Meeting 2011
  276. Joint Group Meeting 2012
  277. Joint Group Meeting 2013
  278. Journal Articles from UCSF
  279. Lab-designed code and programs
  280. Legacy Info
  281. Ligand Enrichment Tutorial
  282. LoadLeveler Chain Jobs
  283. MATLAB
  284. MD Simulation: Protein in Water
  285. MD Simulation: Protein in Water (Pt. 2)
  286. MOE
  287. MPICH
  288. Main Page
  289. Make Unique script usage
  290. Make surface
  291. Making images for publication
  292. Making images for publication using vmd
  293. Method development
  294. NAMD Amber inputs
  295. NAMD on Seawulf
  296. NAMD to mol2
  297. NAMD tutorial
  298. NOVA
  299. NOVA (Navigation and Optimization for Virtual Assembly)
  300. No t4 step1 inputgen.bash
  301. No t4 step2 equiprod.bash
  302. No t4 step2 min.bash
  303. No t4 step3 inputgen.bash
  304. Nonstandard residues prep
  305. Octave
  306. Optimize Polar Hydrogens
  307. Other Meetings
  308. Outdated Info
  309. PBS Queue
  310. PDFCreator
  311. Parameter List
  312. Parameter List/Explanations
  313. Past Announcements
  314. Pdb to mol2
  315. Per-residue energy decompositions
  316. Ps.m2p
  317. Ptraj
  318. Pylab
  319. RGD
  320. R - Statistical Computing
  321. Reference.vmd.script
  322. Release
  323. Remove waters from trajectories
  324. Rename files in Unix
  325. Research Foundation
  326. Restraint.vmd.script
  327. Restraint01.pdb
  328. Restraint04.pdb
  329. Rigid.in
  330. Rizzo Lab Downloads
  331. Rizzo Lab Information and Tutorials
  332. Rizzo Lab Members and Contact Information
  333. Rizzo Lab Publications
  334. Rizzo Lab Research
  335. Rizzo Lab Weekly Group Meetings
  336. Rotation students Wiki
  337. Rsync
  338. Run.java.csh
  339. SB2010
  340. SB2011 testset
  341. SB2012
  342. SB2021.v1
  343. SDF to mol2
  344. SLURM
  345. Sampling Methods
  346. Scoring Functions
  347. Scp files from cluster to NYBlue
  348. Seawulf Cluster Assessment
  349. Seawulf Items Needed
  350. Seawulf Programs Needed
  351. Secure Shell (ssh)
  352. Sed - Stream Editor in Unix
  353. Semester Checklist
  354. Sequence alignment
  355. Server Administration
  356. Setting up RSA SecureID token
  357. Setting up insurance through Research Foundation
  358. Setup ssh tunnel to NYBlue fen
  359. Showbox.in
  360. Showsph.in
  361. Slick awk tricks
  362. Small Molecule Evolution (DOCK GA)
  363. Sphere Generation
  364. Stony Brook Joint Group Meetings in Computational Structural Biology
  365. Stupid awk tricks
  366. Submitting BlueGene Jobs
  367. TIMD extraction.py
  368. TIMD integration.py
  369. TIMD integration prep.py
  370. Testset Protocols
  371. Tutorials
  372. Ubq md.mdp
  373. Ubq min.mdp
  374. Ubq npt.mdp
  375. Ubq nvt.mdp
  376. Unix
  377. Unix find
  378. Using convert command unix
  379. VMD
  380. Valgrind
  381. Vi
  382. Virtual Screening Protocol
  383. Virtual Screening Protocol on BlueGene (IGF-IR system)
  384. Virtual Screening SOP
  385. Visiting BNL
  386. Vmd.rmsd.csh
  387. Ways to remove the first line
  388. Which Unix Distribution?
  389. Wiki Editing
  390. With t4 step1 inputgen.bash
  391. With t4 step2 equiprod.bash
  392. With t4 step2 min.bash
  393. With t4 step3 inputgen.bash
  394. X-Win32
  395. Xmgrace
  396. ZINC12 Database
  397. ZINC15 Database
  398. ZINC Database

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