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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

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