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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. 200 Codes DoorDash Gift Card Code Generator Unused 2024 Update No Human Verification
  22. 2010-2011 AMS-532 Fall-Spring
  23. 2010-2011 GRD-500 Fall-Spring
  24. 2010 AMBER Tutorial with Biotin and Streptavidin
  25. 2010 AMS-535 Fall
  26. 2010 AMS-536 Spring
  27. 2010 DOCK tutorial with Streptavidin
  28. 2010 GRD-500 Spring
  29. 2010 LAB
  30. 2010 RCR GROUP MEETING
  31. 2011-2012 AMS-532 Fall-Spring
  32. 2011-2012 GRD-500 Fall-Spring
  33. 2011 AMBER Tutorial with Biotin and Streptavidin
  34. 2011 AMS-535 Fall
  35. 2011 AMS-536 Spring
  36. 2011 DOCK tutorial with Streptavidin
  37. 2011 GRD-500 Spring
  38. 2011 RCR GROUP MEETING
  39. 2012-2013 AMS-532 Fall-Spring
  40. 2012 AMBER Tutorial with Biotin and Streptavidin
  41. 2012 AMS-535 Fall
  42. 2012 AMS-536 Spring
  43. 2012 DOCK tutorial with Streptavidin
  44. 2012 GRD-500 Spring
  45. 2012 RCR GROUP MEETING
  46. 2013-2014 AMS-532 Fall-Spring
  47. 2013 AMBER Tutorial with UMP and OMP
  48. 2013 AMS-535 Fall
  49. 2013 AMS-536 Spring
  50. 2013 DOCK tutorial with Orotodine Monophosphate Decarboxylase
  51. 2013 RCR GROUP MEETING
  52. 2014
  53. 2014-2015 AMS-532 Fall-Spring
  54. 2014 AMBER tutorial with HIV Protease
  55. 2014 AMS-535 Fall
  56. 2014 AMS-536 Spring
  57. 2014 DOCK tutorial with HIV Protease
  58. 2014 RCR GROUP MEETING
  59. 2015-2016 AMS-532 Fall-Spring
  60. 2015 AMBER tutorial with PARP
  61. 2015 AMS-535 Fall
  62. 2015 AMS-536 Spring
  63. 2015 DOCK tutorial with Poly(ADP-ribose) polymerase (PARP)
  64. 2015 RCR GROUP MEETING
  65. 2016-2017 AMS-532 Fall-Spring
  66. 2016 AMBER tutorial with Beta Trypsin
  67. 2016 AMBER tutorial with Thrombin
  68. 2016 AMS-535 Fall
  69. 2016 AMS-536 Spring
  70. 2016 DOCK tutorial with Beta Trypsin
  71. 2016 RCR GROUP MEETING
  72. 2017-2018 AMS-532 Fall-Spring
  73. 2017 AMBER tutorial with 4qmz
  74. 2017 AMS-535 Fall
  75. 2017 AMS-536 Spring
  76. 2017 DOCK tutorial 1 with PDB 4QMZ NEW
  77. 2017 DOCK tutorial 2 with PDB 3GPL NEW
  78. 2017 Denovo design tutorial 1 with PDB 1BJU
  79. 2017 Denovo design tutorial 2 with PDB 4QMZ
  80. 2017 Denovo design tutorial with PDB 1BJU
  81. 2017 Denovo refine tutorial with PDB 1BJU
  82. 2017 Denovo refinement tutorial with PDB 1BJU
  83. 2017 Dock tutorial
  84. 2017 RCR GROUP MEETING
  85. 2017a DOCK tutorial
  86. 2018
  87. 2018-2019 AMS-532 Fall-Spring
  88. 2018 AMBER tutorial with 1c87
  89. 2018 AMBER tutorial with 2nnq
  90. 2018 AMS-535 Fall
  91. 2018 AMS-536 Spring
  92. 2018 DOCK tutorial 1 with PDBID 2NNQ
  93. 2018 DOCK tutorial 2 with PDBID 1C87
  94. 2018 Denovo design tutorial 1 with PDB 2NNQ
  95. 2018 Denovo design tutorial 2 with PDB 1C87
  96. 2018 RCR GROUP MEETING
  97. 2019-2020 AMS-532 Fall-Spring
  98. 2019 AMBER tutorial with PDBID 2BXF
  99. 2019 AMS-535 Fall
  100. 2019 AMS-536 Spring
  101. 2019 Covalent docking tutorial 1 with PDB 2VKG
  102. 2019 Covalent docking tutorial 1 with PDB 5VKG
  103. 2019 DOCK GA tutorial 1 with 2NNQ
  104. 2019 DOCK tutorial 1 with PDBID 2BXF
  105. 2019 DOCK tutorial 2 with PDBID 2P16
  106. 2019 DOCK tutorial 3 with PDBID 3JQZ
  107. 2019 Denovo design tutorial 1 with PDB 2BXF
  108. 2019 Denovo design tutorial 2 with PDB 2P16
  109. 2019 Denovo design tutorial 3 with PDB 3JQZ
  110. 2019 RCR GROUP MEETING
  111. 2020-2021 AMS-532 Fall-Spring
  112. 2020 AMBER tutorial with PDBID 3VJK
  113. 2020 AMS-535 Fall
  114. 2020 AMS-536 Spring
  115. 2020 AMS-536 Spring (original syllabus)
  116. 2020 AMS-536 Spring (revised syllabus)
  117. 2020 DOCK tutorial 1 with PDBID 3VJK
  118. 2020 DOCK tutorial 1 with PDBID XXXX
  119. 2020 DOCK tutorial 2 with PDBID 2GQG
  120. 2020 DOCK tutorial 2 with PDBID XXXX
  121. 2020 DOCK tutorial 3 with PDBID 4F4P
  122. 2020 DOCK tutorial 4 with PDBID 6UZW
  123. 2020 DOCK tutorial 4 with PDBID XXXX
  124. 2020 Denovo tutorial 1 with PDBID 3VJK
  125. 2020 Denovo tutorial 2 with PDBID 2GQG
  126. 2020 Denovo tutorial 3 with PDBID 4F4P
  127. 2020 Denovo tutorial 4 with PDBID 6UZW
  128. 2021-2022 AMS-532 Fall-Spring
  129. 2021 AMBER tutorial 1 with PDBID 1HW9
  130. 2021 AMBER tutorial 3 with PDBID 1S19
  131. 2021 AMS-535 Fall
  132. 2021 AMS-536 Spring
  133. 2021 DOCK tutorial 1 with PDBID 1HW9
  134. 2021 DOCK tutorial 2 with PDBID 2ZD1
  135. 2021 DOCK tutorial 3 with PDBID 1S19
  136. 2021 DOCK tutorial 4 with PDBID 1EFY
  137. 2021 Denovo tutorial 1 with PDBID 1HW9
  138. 2021 Denovo tutorial 2 with PDBID 2ZD1
  139. 2021 Denovo tutorial 3 with PDBID 1S19
  140. 2021 Denovo tutorial 4 with PDBID 1EFY
  141. 2022-2023 AMS-532 Fall-Spring
  142. 2022 AMBER tutorial 1 with PDBID 6ME2
  143. 2022 AMBER tutorial 3 with PDBID 1X70
  144. 2022 AMS-535 Fall
  145. 2022 AMS-536 Spring
  146. 2022 Covalent docking tutorial updated with PDB xxxx
  147. 2022 DOCK tutorial 1 with PDBID 6ME2
  148. 2022 DOCK tutorial 2 with PDBID 4ZUD
  149. 2022 DOCK tutorial 3 with PDBID 1X70
  150. 2022 Denovo tutorial 1 with PDBID 6ME2
  151. 2022 Denovo tutorial 2 with PDBID 4ZUD
  152. 2022 Denovo tutorial 3 with PDBID 1X70
  153. 2022 RCR GROUP MEETING
  154. 2023-2024 AMS-532 Fall-Spring
  155. 2023 AMBER tutorial 1 with PDBID 4S0V
  156. 2023 AMBER tutorial 2 with PDBID 3WZE
  157. 2023 AMBER tutorial 3 with PDBID 2P16
  158. 2023 AMS-535 Fall
  159. 2023 AMS-536 Spring
  160. 2023 DOCK tutorial 1 with PDBID 4S0V
  161. 2023 DOCK tutorial 2 with PDBID 3WZE
  162. 2023 DOCK tutorial 3 with PDBID 2P16
  163. 2023 Denovo tutorial 1 with PDBID 4S0V
  164. 2023 Denovo tutorial 2 with PDBID 3WZE
  165. 2023 Denovo tutorial 3 with PDBID 2P16
  166. 2024-2025 AMS-532 Fall-Spring
  167. 2024 AMBER tutorial 1 with PDBID 2ITO
  168. 2024 AMBER tutorial 2 with PDBID 1NDV
  169. 2024 AMBER tutorial 3 with PDBID 1Y0X
  170. 2024 AMS-535 Fall
  171. 2024 AMS-536 Spring
  172. 2024 DOCK GA tutorial 1 with 1NDV
  173. 2024 DOCK tutorial 1 with PDBID 2ITO
  174. 2024 DOCK tutorial 2 with PDBID 1NDV
  175. 2024 DOCK tutorial 3 with PDBID 1Y0X
  176. 2024 Denovo tutorial 1 with PDBID 2ITO
  177. 2024 Denovo tutorial 3 with PDBID 1Y0X
  178. 2025 AMS-536 Spring
  179. 2025 DOCK GA tutorial 2 with 1XMU
  180. 2025 DOCK tutorial 1 with PDBID 1O86
  181. 2025 DOCK tutorial 2 with PDBID 1XMU
  182. 2025 Denovo tutorial 2 with PDBID 1XMU
  183. 3D Analog Library Generation Using Pubchem and Zinc
  184. AMBER Lipid Tutorials
  185. AMBER TI Tutorials
  186. AMBER Tutorials
  187. AMBER tricks
  188. AMS-531 Laboratory Rotations in Computational Biology
  189. AMS-532: Lab Rotations/Journal Club Guidelines
  190. AMS-532 Guidlines
  191. AMS-532 Journal Club in Computational Biology
  192. AMS-532 Laboratory Rotations and Journal Club in Computational Biology
  193. AMS-535 Introduction to Computational Structural Biology and Drug Design
  194. AMS-536 Molecular Modeling of Biological Molecules
  195. Activating your Seawulf Account
  196. Additional DOCK6 Information
  197. Advanced Dock Utilities
  198. Advanced Dock Utilities/Information
  199. Amber on Seawulf (compilation)
  200. Amber to mol2 (protein)
  201. Amber to pdb
  202. Ams.stonybrook.edu
  203. Analog Library - Pubchem & Zinc
  204. Analysis Tools Repository
  205. Announcements: Fall 2013
  206. Apply for NYBlue
  207. Apply for cluster
  208. Archiving old data
  209. AutoDock4 Benchmark Results
  210. AutoDock4 Pose Reproduction Tutorial
  211. AutoDock Vina Benchmark Results
  212. AutoDock Vina Pose Reproduction Tutorial
  213. Automated Families generation from the Protein Databank
  214. Automated Family generation from PDB
  215. BASH scripting
  216. BOSS Pure Liquid Simulation Notes
  217. Benchmarking Protocols and Lab SOPs
  218. Benchmarking Protocols and Results
  219. Benchmarking Results
  220. Binding Footprint Program
  221. Blocked Standard Error of the Mean
  222. BlueGene
  223. CONGA
  224. CONGA (CONstruction by Genetic Algorithm)
  225. CONGA Parameter List
  226. CVS Commands
  227. C Shell Scripting
  228. Cancer
  229. Chimera
  230. Cluster compilations
  231. Clustering in R
  232. Coming Soon
  233. Common Errors - ctrl M
  234. Compiling Applications for BG/L
  235. Compiling GROMACS on Cluster
  236. Config
  237. Cross Docking SB2024 V1 DOCK6.10 A
  238. DGHYD
  239. DOCK6 POSE Reproduction
  240. DOCK Abbreviations Guide
  241. DOCK Benchmarking
  242. DOCK CV Benchmarking
  243. DOCK CV Development Goals
  244. DOCK CV Input File(s)
  245. DOCK CV Tutorials
  246. DOCK Compilation
  247. DOCK DN Benchmarking
  248. DOCK DN Development Goals
  249. DOCK DN Input File(s)
  250. DOCK DN Parameters
  251. DOCK DN Tutorials
  252. DOCK DN Utilities
  253. DOCK DN Utilities/Info
  254. DOCK Denovo
  255. DOCK Denovo Refinement
  256. DOCK Denovo Run
  257. DOCK GA Developer Progress
  258. DOCK GA Development Goals
  259. DOCK GA Input File(s)
  260. DOCK GA Parameter List
  261. DOCK GA Parameters
  262. DOCK GA Tutorials
  263. DOCK GIST Parameters
  264. DOCK Installation
  265. DOCK NOVA
  266. DOCK Release Objectives
  267. DOCK Tutorials
  268. DOCK VS Benchmarking
  269. DOCK VS Development Goals
  270. DOCK VS Parameters
  271. DOCK VS Tutorials
  272. DOCK VS Utilities
  273. DOCK VS Utilities/Info
  274. Database Enrichment SB2024 V1 DOCK6.10 A
  275. De Novo Design
  276. De Novo Design (DOCK DN)
  277. De Novo Design (previously NOVA)
  278. De novo Benchmarking
  279. De novo DOCK
  280. De novo Developer Progress
  281. Dell 5110cn Printer
  282. Developer's Info Goals
  283. Development Goals Archive
  284. Disulfide.txt
  285. Drug-like organic molecules
  286. Energy Scoring Method in Grid
  287. Ethernet Cables
  288. Example Input Files
  289. Example of an CONGA Input file
  290. Example of an Ensemble Evolution Input file
  291. Example of an Input file
  292. Example of an Single Molecule Evolution Input file
  293. Example scripts
  294. Families in the Protein Databank
  295. Flex.in
  296. Footprint Plot Visualization
  297. Formating your Thesis
  298. Formatting your Thesis
  299. Fourier fit
  300. Fragment Library Generation
  301. GRD-500 Integrity in Science
  302. Gdb (GNU Debugger)
  303. General Dock Development Goals
  304. General Dock Utilities
  305. General Dock Utilities/Info
  306. Genion.mdp
  307. Get Job ids to use for llcancel
  308. Get time estimate for free blocks
  309. Get time for job completion
  310. Getting a BNL Account
  311. Ghostscript
  312. Gnuplot
  313. Grid.in
  314. HIV/AIDS
  315. Histograms in R
  316. How to purchase compounds for Rizzo lab
  317. INSPH
  318. Influenza
  319. Installing DOCK
  320. Installing MSMS for VMD
  321. Integration.pl
  322. Joe and Brian de novo stuff
  323. Joint Group Meeting 2007-2009
  324. Joint Group Meeting 2010
  325. Joint Group Meeting 2011
  326. Joint Group Meeting 2012
  327. Joint Group Meeting 2013
  328. Journal Articles from UCSF
  329. Lab-designed code and programs
  330. Lab SOP
  331. Legacy Info
  332. LoadLeveler Chain Jobs
  333. MATLAB
  334. MD Simulation: Protein in Water
  335. MD Simulation: Protein in Water (Pt. 2)
  336. MOE
  337. MPICH
  338. Main Page
  339. Make Unique script usage
  340. Make surface
  341. Making images for publication
  342. Making images for publication using vmd
  343. Method development
  344. NAMD Amber inputs
  345. NAMD on Seawulf
  346. NAMD to mol2
  347. NAMD tutorial
  348. NOVA
  349. NOVA (Navigation and Optimization for Virtual Assembly)
  350. No t4 step1 inputgen.bash
  351. No t4 step2 equiprod.bash
  352. No t4 step2 min.bash
  353. No t4 step3 inputgen.bash
  354. Nonstandard residues prep
  355. Octave
  356. Optimize Polar Hydrogens
  357. Other Meetings
  358. Outdated Info
  359. PBS Queue
  360. PDFCreator
  361. Parameter List
  362. Parameter List/Explanations
  363. Past Announcements
  364. Pdb to mol2
  365. Per-residue energy decompositions
  366. Pose Reproduction SB2024 V1 DOCK6.10 A
  367. Ps.m2p
  368. Ptraj
  369. Pylab
  370. RGD
  371. R - Statistical Computing
  372. Reference.vmd.script
  373. Release
  374. Remove waters from trajectories
  375. Rename files in Unix
  376. Research Foundation
  377. Restraint.vmd.script
  378. Restraint01.pdb
  379. Restraint04.pdb
  380. Rigid.in
  381. Ringo.ams.stonybrook.edu
  382. Rizzo Lab Downloads
  383. Rizzo Lab General Information for Lab Members
  384. Rizzo Lab Information and Tutorials
  385. Rizzo Lab Members and Contact Information
  386. Rizzo Lab Publications
  387. Rizzo Lab Research
  388. Rizzo Lab Weekly Group Meetings
  389. Rotation students Wiki
  390. Rsync
  391. Run.java.csh
  392. SB2010
  393. SB2011 testset
  394. SB2012
  395. SB2021.v1
  396. SDF to mol2
  397. SLURM
  398. Sampling Methods
  399. Scoring Functions
  400. Scp files from cluster to NYBlue
  401. Seawulf Cluster Assessment
  402. Seawulf Items Needed
  403. Seawulf Programs Needed
  404. Secure Shell (ssh)
  405. Sed - Stream Editor in Unix
  406. Semester Checklist
  407. Sequence alignment
  408. Server Administration
  409. Setting up RSA SecureID token
  410. Setting up insurance through Research Foundation
  411. Setup ssh tunnel to NYBlue fen
  412. Showbox.in
  413. Showsph.in
  414. Slick awk tricks
  415. Small Molecule Evolution (DOCK GA)
  416. Sphere Generation
  417. Stony Brook Joint Group Meetings in Computational Structural Biology
  418. Stonybrook
  419. Stupid awk tricks
  420. Submitting BlueGene Jobs
  421. TIMD extraction.py
  422. TIMD integration.py
  423. TIMD integration prep.py
  424. Test Page
  425. Test Set Construction SB2024 V1 DOCK6.10 A
  426. Test Set Tutorial
  427. Testset Objectives
  428. Testset Protocols
  429. Torsion environment
  430. Tutorials
  431. Ubq md.mdp
  432. Ubq min.mdp
  433. Ubq npt.mdp
  434. Ubq nvt.mdp
  435. Unix
  436. Unix find
  437. Useful Slurm Commands
  438. Using convert command unix
  439. VMD
  440. Valgrind
  441. Vi
  442. Virtual Screening Compound Ordering SOP
  443. Virtual Screening Protocol
  444. Virtual Screening Protocol on BlueGene (IGF-IR system)
  445. Visiting BNL
  446. Vmd.rmsd.csh
  447. Ways to remove the first line
  448. Which Unix Distribution?
  449. Wiki Editing
  450. With t4 step1 inputgen.bash
  451. With t4 step2 equiprod.bash
  452. With t4 step2 min.bash
  453. With t4 step3 inputgen.bash
  454. X-Win32
  455. Xmgrace
  456. ZINC12 Database
  457. ZINC15 Database
  458. ZINC Database

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