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  • Rizzo Lab Information and Tutorials
    * [[How to purchase compounds for Rizzo lab]]
    3 KB (307 words) - 09:56, 16 June 2021
  • Rizzo Lab Weekly Group Meetings
    2 KB (329 words) - 11:13, 15 August 2022
  • Rizzo Lab-specific Information and Tutorials
    #REDIRECT [[Rizzo Lab Information and Tutorials]]
    49 bytes (6 words) - 14:31, 5 February 2008
  • Robert C. Rizzo Research Group
    23 bytes (3 words) - 15:29, 5 February 2008
  • Rizzo Lab Contact Information
    #REDIRECT [[Rizzo Lab Members and Contact Information]]
    55 bytes (7 words) - 11:45, 2 March 2008
  • Rizzo Lab Members and Contact Information
    ! style="width:50%" |Robert C. Rizzo Website: https://ringo.ams.stonybrook.edu/~rizzo
    6 KB (715 words) - 11:12, 10 April 2023
  • Rizzo Lab Wiki
    23 bytes (3 words) - 11:21, 2 March 2008
  • Rizzo Lab Downloads
    **Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free **Mukherjee, S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility
    1 KB (161 words) - 22:48, 11 May 2023
  • Rizzo Lab Research
    Under the broad umbrella of Computational Structural Biology, research in the Rizzo lab involves Development, Validation, and Application of improved atomic-le ...ion Databases, ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Downloads, and (c) Rizzo Group Online Tutorials, ringo.ams.sunysb.edu/index.php/DOCK_Tutorials. Imp
    9 KB (1,258 words) - 15:50, 5 November 2020
  • Rizzo Lab Publications
    # Bausch, J. W.; '''Rizzo, R. C.'''; Sneddon, L. G.; Wille, A. E.; Williams, R. E. An ''Ab Initio''/I # '''Rizzo, R. C.'''; Jorgensen, W. L. OPLS All-Atom Model for Amines: Resolution of t
    16 KB (2,490 words) - 11:13, 18 October 2022
  • How to purchase compounds for Rizzo lab
    This is a guide for Rizzo lab members to purchasing compounds through Molport for testing. ...ess to Wolfmart. You can request access through Andrea Curran and with Dr. Rizzo's permission.
    2 KB (238 words) - 11:05, 5 May 2021

Page text matches

  • Main Page
    == Rizzo Lab Wiki: Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage == *[[Rizzo Lab Research]]
    588 bytes (71 words) - 12:32, 15 September 2015
  • Rizzo Lab Information and Tutorials
    * [[How to purchase compounds for Rizzo lab]]
    3 KB (307 words) - 09:56, 16 June 2021
  • Stony Brook Joint Group Meetings in Computational Structural Biology
    ...fgreen/ Green], [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/index.html Rizzo], [http://simmerlinglab.org Simmerling], [http://www.sunysb.edu/chemistry/ For the Rizzo lab members do the following for reimbursement:
    2 KB (371 words) - 12:03, 12 March 2012
  • 2008 DOCK tutorial with Gleevec
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. [[http://rizzo.ams.sunysb.edu/~sudipto/1XBB.grid.tar.bz2 Sample prepared grids]]
    14 KB (2,032 words) - 10:30, 19 May 2011
  • 2008 AMBER tutorial
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]].
    16 KB (2,476 words) - 11:01, 31 January 2011
  • Grid.in
    vdw_definition_file /home/rizzo/AMS536software/dock6/parameters/vdw_AMBER_parm99.defn
    692 bytes (61 words) - 16:53, 20 February 2008
  • Rigid.in
    vdw_defn_file /home/rizzo/AMS536software/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /home/rizzo/AMS536software/dock6/parameters/flex.defn
    3 KB (206 words) - 16:30, 5 June 2008
  • Flex.in
    vdw_defn_file /home/rizzo/AMS536software/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /home/rizzo/AMS536software/dock6/parameters/flex.defn
    4 KB (255 words) - 17:17, 11 February 2008
  • AMS-532 Laboratory Rotations and Journal Club in Computational Biology
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    7 KB (1,038 words) - 15:18, 5 August 2013
  • Getting a BNL Account
    There are two acounts every one in the rizzo group should have:
    210 bytes (34 words) - 11:28, 1 May 2015
  • Apply for cluster
    # Justification of visit/assignment "Member of Robert C. Rizzo Lab, Stony Brook Univ."
    3 KB (531 words) - 13:53, 1 May 2015
  • 2008 DOCK tutorial with 1LAH
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]].
    12 KB (1,877 words) - 11:02, 31 January 2011
  • Rizzo Lab Members and Contact Information
    ! style="width:50%" |Robert C. Rizzo Website: https://ringo.ams.stonybrook.edu/~rizzo
    6 KB (715 words) - 11:12, 10 April 2023
  • BOSS Pure Liquid Simulation Notes
    ...the calculations are in my home directory on the Mathlab computers: /home/rizzo/AMS536projects/pureliquid. We will also discuss the details in class. Und Make copies from /home/rizzo/AMS536projects/pureliquid to your directory and edit the $MYdir parameter i
    6 KB (964 words) - 14:56, 27 February 2008
  • AMS-535 Introduction to Computational Structural Biology and Drug Design
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    6 KB (830 words) - 17:35, 28 August 2022
  • AMS-536 Molecular Modeling of Biological Molecules
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching) </center> === | '''Instructor''' || Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]
    7 KB (905 words) - 17:13, 10 January 2023
  • 2006-2007 AMS-532 Fall-Spring
    | 2006.09.26 || Mukherjee, Sudipto || Rizzo Group || scoring functions || Wang, R.; Lu, Y.; Wang, S., Comparative evalu | 2006.10.03 || Han, Ji || Rizzo, Simmerling, Green || MM-GBSA validation || Kuhn, B.; Gerber, P.; Schulz-Ga
    5 KB (689 words) - 13:22, 15 September 2008
  • 2008 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf pr
    5 KB (654 words) - 12:44, 1 June 2016
  • 2007-2008 AMS-532 Fall-Spring
    | 2007.09.28 || Barsegian, Garen || Deng, Rizzo, Simmerling || dynamic positional info. || Jaeger, J.; Reinitz, J. On the d | 2007.10.12 || Goyal, Rashi || Rizzo Group|| avian influenza || Russell, R.J. ''et al''. The structure of H5N1 a
    5 KB (722 words) - 17:38, 10 September 2008
  • MATLAB
    == Useful Matlab Functions written by Rizzo group ==
    2 KB (330 words) - 18:51, 14 January 2013
  • 2008-2009 AMS-532 Fall-Spring
    | 2008.09.12 || Balius, Trent || Rizzo || Inverse Design of ligands || Altman, M. D.; et al., HIV-1 protease inhib | 2008.10.24 || Goyal, Rashi || Rizzo || Relaxed Complex Scheme || Amaro, R.E. ; Baron, R. & McCammon, J.A. An im
    5 KB (647 words) - 23:53, 10 May 2009
  • 2008 AMS-535 Fall
    [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2007.ams535.example. ...ng/AMS532_AMS535_AMS536/Presentations/2008.09.08.ams535.rizzo.lect.001.pdf Rizzo, R.]
    26 KB (3,589 words) - 09:52, 6 August 2013
  • Testset Protocols
    Please consult page [[Rizzo Lab Downloads]] for the most up-to-date Rizzo lab test sets.
    7 KB (752 words) - 13:12, 4 February 2019
  • Joint Group Meeting 2007-2009
    | 12th Feb 2008 || Sudipto Mukherjee || Rizzo || Docking Testset and Improvements in Docking Protocol | 08th Jul 2008 || Trent Balius || Rizzo || Inhibition and Conformational Shifts of EGFR Tyrosine Kinase Domain Usin
    2 KB (319 words) - 12:29, 7 April 2010
  • Which Unix Distribution?
    On rizzo.ams.sunysb.edu this produces
    233 bytes (34 words) - 16:36, 8 September 2009
  • Past Announcements
    :# On the day of your presentation, '''please email me and Dr. Rizzo the following''': (a) three potential exam questions and (b) presentation i :#The presentation list has been updated. Dr. Rizzo and I have agreed to keep ''Replica Exchange'' as is.
    8 KB (1,353 words) - 22:11, 9 December 2010
  • Joint Group Meeting 2010
    | 20 May 2010 || Sudipto Mukherjee || Rizzo || Docking Validation Resources: Protein Family and Ligand Flexibility Expe
    903 bytes (107 words) - 13:57, 19 October 2010
  • 2010 AMS-535 Fall
    * [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ams535.example.quest ...ng/AMS532_AMS535_AMS536/Presentations/2010.09.01.ams535.rizzo.lect.001.pdf Rizzo, R.]
    27 KB (3,741 words) - 09:59, 6 August 2013
  • Virtual Screening Protocol
    In this document, the current Rizzo group protocol will be described in detail. This protocol has be through s
    15 KB (1,949 words) - 12:10, 4 December 2018
  • 2010 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.student.info.doc
    6 KB (744 words) - 17:23, 5 August 2013
  • 2010 AMBER Tutorial with Biotin and Streptavidin
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]]. * Note that is only applies to AMS536 (or Rizzo lab rotation) students and is specific for our computer setup.
    34 KB (5,393 words) - 10:22, 28 February 2012
  • 2010 DOCK tutorial with Streptavidin
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. This tutorial was developed collabora
    22 KB (2,471 words) - 18:54, 7 May 2012
  • 2009 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.student.info.doc
    6 KB (696 words) - 17:22, 5 August 2013
  • Rizzo Lab Downloads
    **Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free **Mukherjee, S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility
    1 KB (161 words) - 22:48, 11 May 2023
  • 2009 AMS-535 Fall
    [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2007.ams535.example. ...ng/AMS532_AMS535_AMS536/Presentations/2009.09.02.ams535.rizzo.lect.001.pdf Rizzo, R.]
    28 KB (3,785 words) - 09:57, 6 August 2013
  • 2009 AMBER tutorial with Trpcage
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]]. *[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/MDtutorial_Amber10.pdf MD
    25 KB (4,118 words) - 11:01, 31 January 2011
  • 2009 DOCK tutorial with neuraminidase
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. vdw_definition_file /home/rizzo/AMS536software/dock6/parameters/vdw_AMBER_parm99.defn
    32 KB (3,664 words) - 11:02, 31 January 2011
  • 2009-2010 AMS-532 Fall-Spring
    | 2009.11.11 || Balius, Trent || Rizzo Group || Clustering MD simulations || Shao, J., et al.; Clustering molecula | 2010.04.14 || Falk, Adam|| Rizzo|| Thermodynamic Integration|| Steinbrecher, T., Mobley, D.L., Case, D.A.; N
    5 KB (591 words) - 12:32, 12 August 2010
  • Rotation students Wiki
    ...paragraph describing the project you will be doing during your rotation in Rizzo Group. Also include the specific programs (e.g. DOCK, AMBER, NAMD) you wil ...n etc). In the second section, indicate “'''Laboratory Rotation Student: Rizzo Research Group'''” under “Title of Proposal”. The paragraph describin
    1 KB (209 words) - 15:02, 8 December 2009
  • 2010-2011 AMS-532 Fall-Spring
    ...o professor Rizzo and his students （Trent Balius and Lingling Jiang）. Rizzo lab is located in Room 3-129, Math Tower. | 2010.11.17 || Balius, Trent || Rizzo || Drug design ||
    10 KB (1,385 words) - 15:22, 5 August 2013
  • Cluster compilations
    Every time a member of the Rizzo Group compiles a program on Cluster we should write a README file that docu ## Runing of the amber test and a rizzo lab bench mark imply that sander.MPI is working (2010/09/15).
    2 KB (287 words) - 16:44, 15 September 2010
  • 2011 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.student.info.doc
    6 KB (754 words) - 17:23, 5 August 2013
  • 2011 AMBER Tutorial with Biotin and Streptavidin
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]]. cd ~rizzo/AMBER_Tutorial/000.AMBERFILES .
    40 KB (6,379 words) - 15:51, 25 March 2011
  • 2011 DOCK tutorial with Streptavidin
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. This tutorial is based on the [[2010
    20 KB (2,410 words) - 18:55, 7 May 2012
  • Fourier fit
    % Robert C. Rizzo Research Group
    2 KB (272 words) - 08:23, 6 May 2011
  • Per-residue energy decompositions
    Here are some tutorials on the Rizzo lab wiki for running MD: Here is also some information on NAMD from the rizzo lab wiki:
    7 KB (912 words) - 10:31, 17 September 2013
  • Nonstandard residues prep
    loadamberparams gaff.dat.rizzo
    13 KB (1,725 words) - 21:40, 23 May 2011
  • Rizzo Lab Research
    Under the broad umbrella of Computational Structural Biology, research in the Rizzo lab involves Development, Validation, and Application of improved atomic-le ...ion Databases, ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Downloads, and (c) Rizzo Group Online Tutorials, ringo.ams.sunysb.edu/index.php/DOCK_Tutorials. Imp
    9 KB (1,258 words) - 15:50, 5 November 2020
  • HIV/AIDS
    ...ct. Func. Bioinformatics, 2007, 67, 630-642. [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo015.pdf PDF] .../pubs.acs.org/doi/abs/10.1021/bi901915g WEB] [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo020.pdf PDF]
    702 bytes (92 words) - 14:52, 24 May 2011
  • Cancer
    .... Bioorg. Med. Chem. Lett., 2009, 19, 47-50. [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo017.pdf PDF] .../pubs.acs.org/doi/abs/10.1021/bi900729a WEB] [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo019.pdf PDF]
    801 bytes (113 words) - 14:31, 24 May 2011
  • Influenza
    ...J. Chem. Theory Comput., 2008 ,4, 1526-1540. [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo016.pdf PDF]
    290 bytes (39 words) - 14:32, 24 May 2011
  • 2012 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc
    7 KB (962 words) - 17:24, 5 August 2013
  • 2011 AMS-535 Fall
    #Feel free to discuss your assigned topics with Rizzo lab members. * [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ams535.example.quest
    28 KB (3,894 words) - 10:00, 6 August 2013
  • 2011-2012 AMS-532 Fall-Spring
    | 2011.10.05 || Fochtman, Brian || Rizzo || topic || Efficient Inclusion of Receptor Flexibility in Grid-Based Prote ...ent chairs by professor Michael Hadjiargyrou [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2
    10 KB (1,428 words) - 16:08, 5 August 2013
  • Joint Group Meeting 2011
    | 21 Nov 2011 || Trent Balius|| Rizzo Group || Development and Application of a Rescoring Tool for Docking and Dr
    631 bytes (80 words) - 11:17, 8 December 2011
  • Joint Group Meeting 2013
    | 18 Feb 2013 || name || Rizzo Group || title
    980 bytes (120 words) - 12:04, 12 March 2012
  • 2015 DOCK tutorial with Poly(ADP-ribose) polymerase (PARP)
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    32 KB (4,231 words) - 14:16, 25 March 2015
  • 2012 DOCK tutorial with Streptavidin
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.unilang.org echo "loadamberparams ../rizzo_amber7.ionparms/gaff.dat.rizzo" >> tleap.$lig.in
    54 KB (7,585 words) - 12:22, 24 October 2012
  • 2012 AMBER Tutorial with Biotin and Streptavidin
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]]. loadamberparams rizzo_amber7.ionparms/gaff.dat.rizzo
    50 KB (7,758 words) - 11:31, 26 March 2014
  • Rizzo Lab Publications
    # Bausch, J. W.; '''Rizzo, R. C.'''; Sneddon, L. G.; Wille, A. E.; Williams, R. E. An ''Ab Initio''/I # '''Rizzo, R. C.'''; Jorgensen, W. L. OPLS All-Atom Model for Amines: Resolution of t
    16 KB (2,490 words) - 11:13, 18 October 2022
  • 2013-2014 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    12 KB (1,647 words) - 16:25, 9 April 2014
  • Formating your Thesis
    For more tutorials from the Rizzo Group go here: [[Rizzo Lab Information and Tutorials]] ...lius.Dissertation.pdf] (SBU) or Rob Rizzo's [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo000.pdf] (yale).
    2 KB (404 words) - 23:33, 9 January 2013
  • 2012 AMS-535 Fall
    * [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ams535.example.quest ...ng/AMS532_AMS535_AMS536/Presentations/2012.08.29.ams535.rizzo.lect.001.pdf Rizzo, R.]
    28 KB (3,783 words) - 10:03, 6 August 2013
  • SB2012
    For more Rizzo Lab downloads: [[Rizzo Lab Downloads]] ...er of the lab if you face any problems. Contact information can be found [[Rizzo Lab Members and Contact Information|here]]. <BR>
    8 KB (1,129 words) - 15:24, 6 September 2019
  • 2012-2013 AMS-532 Fall-Spring
    | 2012.09.05 || Zhou, Yuchen || Rizzo || Topic || Armstrong, MS., et al., ElectroShape: fast molecular similarity | 2012.09.26 || Krantsevich, Nikolay || Rizzo || Topic|| Barrciro, G., et al., From Docking False-Positive to Active Anti
    4 KB (522 words) - 17:11, 23 January 2014
  • SB2010
    For more Rizzo Lab downloads: [[Rizzo Lab Downloads]] ...er of the lab if you face any problems. Contact information can be found [[Rizzo Lab Members and Contact Information|here]].<BR>
    10 KB (1,400 words) - 10:28, 10 June 2019
  • 2013 DOCK tutorial with Orotodine Monophosphate Decarboxylase
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    33 KB (4,293 words) - 17:26, 14 January 2015
  • 2013 AMBER Tutorial with UMP and OMP
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]].
    36 KB (5,444 words) - 16:54, 6 January 2015
  • 2013 AMS-535 Fall
    ...ng/AMS532_AMS535_AMS536/Presentations/2013.08.28.ams535.rizzo.lect.001.pdf Rizzo, R.] 1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgen
    25 KB (3,325 words) - 11:57, 7 April 2014
  • GRD-500 Integrity in Science
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    4 KB (630 words) - 16:00, 5 August 2013
  • AMS-532 Journal Club in Computational Biology
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]
    8 KB (1,062 words) - 11:27, 24 August 2022
  • 2014 DOCK tutorial with HIV Protease
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    40 KB (4,687 words) - 18:05, 17 December 2014
  • 2014 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc
    6 KB (820 words) - 15:18, 11 March 2014
  • DGHYD
    and 11 monatomic ions as described in Rizzo et al. ''JCTC'' '''2006''' 2 (1), 128-139 [http://pubs.acs.org/doi/abs/10 ...er of the lab if you face any problems. Contact information can be found [[Rizzo Lab Members and Contact Information|here]].
    2 KB (279 words) - 16:47, 6 February 2019
  • 2014 AMBER tutorial with HIV Protease
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]]. ...doff rizzo_amber7.ionparms/ions.lib #Loading Rob Rizzo's ion parameters
    33 KB (5,066 words) - 21:14, 23 April 2014
  • Announcements: Fall 2013
    #On Mon. 11/25, Professor Rizzo will go over quiz problems in class. Don't forget to bring your all four qu * [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ams535.example.quest
    2 KB (284 words) - 10:27, 7 April 2014
  • AMS-531 Laboratory Rotations in Computational Biology
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]
    13 KB (1,796 words) - 11:57, 21 October 2022
  • 2014 AMS-535 Fall
    ...ng/AMS532_AMS535_AMS536/Presentations/2014.08.27.ams535.rizzo.lect.001.pdf Rizzo, R.] 1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgen
    25 KB (3,386 words) - 11:41, 12 January 2015
  • 2014-2015 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    12 KB (1,680 words) - 08:36, 25 March 2015
  • 2015 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.temp
    7 KB (894 words) - 14:55, 4 May 2015
  • 2015 AMBER tutorial with PARP
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]].
    25 KB (3,938 words) - 12:53, 26 June 2019
  • 2015-2016 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    13 KB (1,834 words) - 15:47, 10 August 2016
  • 2015 AMS-535 Fall
    ...ng/AMS532_AMS535_AMS536/Presentations/2015.08.26.ams535.rizzo.lect.001.pdf Rizzo, R.] 1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgen
    26 KB (3,499 words) - 12:42, 12 August 2016
  • Joe and Brian de novo stuff
    Generic fragment library is unchanged (/gpfs/projects/rizzo/leprentis/gen-frags-12) /gpfs/projects/rizzo/leprentis/zinc1_ancs_freq
    20 KB (2,576 words) - 13:37, 20 June 2017
  • 2016 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.temp
    7 KB (856 words) - 15:42, 19 February 2019
  • 2016 DOCK tutorial with Beta Trypsin
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    44 KB (4,474 words) - 17:53, 30 January 2017
  • 2016 AMBER tutorial with Thrombin
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]].
    614 bytes (75 words) - 14:16, 6 April 2016
  • 2016 AMBER tutorial with Beta Trypsin
    For additional Rizzo Lab tutorials see [[AMBER Tutorials]].
    23 KB (3,277 words) - 14:51, 12 May 2016
  • 2016 AMS-535 Fall
    ...ng/AMS532_AMS535_AMS536/Presentations/2016.08.31.ams535.rizzo.lect.001.pdf Rizzo, R.] 1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgen
    26 KB (3,580 words) - 14:23, 8 December 2016
  • 2016-2017 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    12 KB (1,708 words) - 10:28, 11 July 2017
  • 2017 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.temp
    7 KB (849 words) - 16:21, 10 April 2017
  • 2017-2018 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    12 KB (1,749 words) - 11:12, 25 August 2018
  • 2017 Dock tutorial
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    5 KB (792 words) - 17:47, 1 February 2017
  • 2017 DOCK tutorial 1 with PDB 4QMZ NEW
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    65 KB (5,888 words) - 18:10, 8 March 2017
  • 2017a DOCK tutorial
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    5 KB (776 words) - 16:56, 6 February 2017
  • 2017 DOCK tutorial 2 with PDB 3GPL NEW
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    45 KB (4,011 words) - 17:59, 8 March 2017
  • De novo Developer Progress
    This is the Rizzo lab wiki page for coordinating bugs and progress on the de novo project. === Valgrind clean version of the code on cluster that Rizzo lab should be using: ===
    7 KB (1,002 words) - 12:53, 4 February 2019
  • 2018 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.temp
    7 KB (860 words) - 15:24, 26 March 2018
  • 2017 AMS-535 Fall
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    27 KB (3,628 words) - 12:58, 20 August 2020
  • 2018 DOCK tutorial 2 with PDBID 1C87
    For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.o
    55 KB (5,122 words) - 15:12, 12 November 2018
  • 2018-2019 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    12 KB (1,687 words) - 16:45, 17 August 2021
  • 2018 AMS-535 Fall
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    28 KB (3,766 words) - 21:54, 3 December 2018
  • 2019 AMS-536 Spring
    | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.temp
    7 KB (971 words) - 12:08, 22 January 2020
  • Formatting your Thesis
    For more tutorials from the Rizzo Group go here: [[Rizzo Lab Information and Tutorials]] ...lius.Dissertation.pdf] (SBU) or Rob Rizzo's [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/publications/rizzo000.pdf] (yale).
    2 KB (404 words) - 12:10, 4 February 2019
  • DOCK DN Development Goals
    This is the Rizzo lab wiki page for coordinating bugs and progress on the de novo project. === Valgrind clean version of the code on cluster that Rizzo lab should be using: ===
    7 KB (1,087 words) - 11:37, 17 February 2022
  • DOCK Release Objectives
    # Rizzo coefficient
    1 KB (188 words) - 14:39, 16 May 2022
  • 2019 AMS-535 Fall
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    28 KB (3,743 words) - 13:01, 20 August 2020
  • 2019 DOCK GA tutorial 1 with 2NNQ
    ...n_env_combination/combine_torenv.py 2NNQ.fraglib_torenv.dat /gpfs/projects/rizzo/zzz.programs/dock6.10_2019.06.18/parameters/fraglib_torenv.dat ...a_fraglib_scaffold_file /gpfs/projects/rizzo/zzz.programs/dock6.10_2019.06.14/parameters /fraglib_ga_scaffold.mol2
    11 KB (997 words) - 13:02, 25 June 2019
  • 2019-2020 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
    3 KB (402 words) - 15:18, 19 August 2020
  • 2020 AMS-535 Fall
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    49 KB (6,825 words) - 19:17, 8 September 2021
  • Analysis Tools Repository
    4) A link to the necessary scripts or code on the Rizzo Lab Github.
    6 KB (616 words) - 14:14, 3 February 2020
  • 2020 AMS-536 Spring (revised syllabus)
    | '''Supervisor''' || Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu] ...be evaluated by 3 course participants and a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.536.present
    22 KB (3,018 words) - 16:29, 27 April 2020
  • 2020 DOCK tutorial 2 with PDBID 2GQG
    vdw_defn_file /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex.defn
    61 KB (5,514 words) - 14:49, 11 March 2020
  • 2020 AMS-536 Spring (original syllabus)
    | '''Supervisor''' || Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu] *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.temp
    13 KB (1,742 words) - 10:20, 19 March 2020
  • DOCK6 POSE Reproduction
    NOTE: The dock6 with simplex minimized script is located in /gpfs/projects/rizzo/slaverty/dock_pose_4_15_20_copy/FLX_pak.sh ...read for assigning ions, this scripts reads from yuchzhuo, /gpfs/projects/rizzo/slaverty/dock_pose_4_15_20_copy/bickel_laverty_calculate_dock6_results_yuch
    4 KB (701 words) - 12:16, 16 August 2020
  • Ligand Enrichment Tutorial
    ...torial is to develop a uniform method to test ligand enrichment across the Rizzo lab with the DOCK software. receptor_site_file /gpfs/projects/rizzo/ccorbo/2020_DUDE_0.3_gridspacing/DUDE_Good_to_go/1Q4X/1Q4X.rec.clust.close.
    15 KB (1,474 words) - 12:22, 15 July 2020
  • AutoDock4 Pose Reproduction Tutorial
    The purpose of this tutorial is to provide members of the Rizzo lab a way to benchmark the AutoDock4 software to compare the Pose Reproduct bash ./../run001.AutoDock4.system.prep.sh /gpfs/projects/rizzo/yuchzhou/RCR/DOCK_testset/clean.systems.all ../AutoDock4_Tutorial
    14 KB (2,352 words) - 12:25, 12 August 2020
  • AutoDock Vina Pose Reproduction Tutorial
    bash ./../run001.AutoDock4.system.prep.sh /gpfs/projects/rizzo/yuchzhou/RCR/DOCK_testset/clean.systems.all ../AutoDock4_Tutorial ...laverty_autodock_runs/pdbqt_to_mol2_vina.sh 9 Vina_Tutorial /gpfs/projects/rizzo/yuchzhou/RCR/DOCK_testset/clean.systems.all
    7 KB (1,145 words) - 10:24, 12 August 2020
  • 2020-2021 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]
    10 KB (1,371 words) - 14:49, 5 November 2020
  • 2021 AMS-536 Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching) </center> === | '''Instructor''' || Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]
    19 KB (2,656 words) - 15:17, 17 August 2021
  • How to purchase compounds for Rizzo lab
    This is a guide for Rizzo lab members to purchasing compounds through Molport for testing. ...ess to Wolfmart. You can request access through Andrea Curran and with Dr. Rizzo's permission.
    2 KB (238 words) - 11:05, 5 May 2021
  • Virtual Screening SOP
    ...ing_Protocols our GitHub repository], you will schedule a meeting with Dr. Rizzo and your collaborators to pick compounds; only then you should pay close at Professor Robert C. Rizzo
    4 KB (697 words) - 14:03, 16 June 2021
  • 2021-2022 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]
    19 KB (2,733 words) - 12:51, 1 December 2021
  • 2021 AMS-535 Fall
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    51 KB (7,035 words) - 21:11, 3 December 2021
  • 2022 AMS-536 Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching) </center> === | '''Instructor''' || Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]
    19 KB (2,596 words) - 11:40, 21 April 2022
  • SB2021.v1
    For more Rizzo Lab downloads: [[Rizzo Lab Downloads]]
    5 KB (767 words) - 01:22, 19 November 2021
  • 2022 AMS-535 Fall
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
    51 KB (7,102 words) - 22:15, 18 November 2022
  • 2022-2023 AMS-532 Fall-Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === |Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com]
    20 KB (2,763 words) - 14:57, 30 November 2022
  • Developer's Info Goals
    ...them to any of the current graduate students or post-docs listed on the [[Rizzo Lab Members and Contact Information|Contact]] page. If they don't know an a
    13 KB (1,902 words) - 11:13, 24 January 2023
  • 2023 AMS-536 Spring
    === <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching) </center> === | '''Instructor''' || Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]
    19 KB (2,681 words) - 10:02, 17 April 2023
  • Development Goals Archive
    |MPI wrapper for 192 processors (8 nodes) for testsets on rizzo cluster || Dwight & Lauren || This is the Rizzo lab wiki page for coordinating bugs and progress on the de novo project.
    6 KB (933 words) - 10:10, 25 October 2022
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