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2006-2007 AMS-532 Fall-Spring
2007-2008 AMS-532 Fall-Spring
2008-2009 AMS-532 Fall-Spring
2008-2009 LAB
2008 AMBER tutorial
2008 AMS-535 Fall
2008 AMS-536 Spring
2008 DOCK tutorial with 1LAH
2008 DOCK tutorial with Gleevec
2008 RCR GROUP MEETING
2008 Spring
2009-2010 AMS-532 Fall-Spring
2009-2010 GRD-500 Fall-Spring
2009 AMBER tutorial with Trpcage
2009 AMS-535 Fall
2009 AMS-536 Spring
2009 DOCK tutorial with neuraminidase
2009 RCR GROUP MEETING
200 Codes DoorDash Gift Card Code Generator Unused 2024 Update No Human Verification
2010-2011 AMS-532 Fall-Spring
2010-2011 GRD-500 Fall-Spring
2010 AMBER Tutorial with Biotin and Streptavidin
2010 AMS-535 Fall
2010 AMS-536 Spring
2010 DOCK tutorial with Streptavidin
2010 GRD-500 Spring
2010 LAB
2010 RCR GROUP MEETING
2011-2012 AMS-532 Fall-Spring
2011-2012 GRD-500 Fall-Spring
2011 AMBER Tutorial with Biotin and Streptavidin
2011 AMS-535 Fall
2011 AMS-536 Spring
2011 DOCK tutorial with Streptavidin
2011 GRD-500 Spring
2011 RCR GROUP MEETING
2012-2013 AMS-532 Fall-Spring
2012 AMBER Tutorial with Biotin and Streptavidin
2012 AMS-535 Fall
2012 AMS-536 Spring
2012 DOCK tutorial with Streptavidin
2012 GRD-500 Spring
2012 RCR GROUP MEETING
2013-2014 AMS-532 Fall-Spring
2013 AMBER Tutorial with UMP and OMP
2013 AMS-535 Fall
2013 AMS-536 Spring
2013 DOCK tutorial with Orotodine Monophosphate Decarboxylase
2013 RCR GROUP MEETING
2014
2014-2015 AMS-532 Fall-Spring
2014 AMBER tutorial with HIV Protease
2014 AMS-535 Fall
2014 AMS-536 Spring
2014 DOCK tutorial with HIV Protease
2014 RCR GROUP MEETING
2015-2016 AMS-532 Fall-Spring
2015 AMBER tutorial with PARP
2015 AMS-535 Fall
2015 AMS-536 Spring
2015 DOCK tutorial with Poly(ADP-ribose) polymerase (PARP)
2015 RCR GROUP MEETING
2016-2017 AMS-532 Fall-Spring
2016 AMBER tutorial with Beta Trypsin
2016 AMBER tutorial with Thrombin
2016 AMS-535 Fall
2016 AMS-536 Spring
2016 DOCK tutorial with Beta Trypsin
2016 RCR GROUP MEETING
2017-2018 AMS-532 Fall-Spring
2017 AMBER tutorial with 4qmz
2017 AMS-535 Fall
2017 AMS-536 Spring
2017 DOCK tutorial 1 with PDB 4QMZ NEW
2017 DOCK tutorial 2 with PDB 3GPL NEW
2017 Denovo design tutorial 1 with PDB 1BJU
2017 Denovo design tutorial 2 with PDB 4QMZ
2017 Denovo design tutorial with PDB 1BJU
2017 Denovo refine tutorial with PDB 1BJU
2017 Denovo refinement tutorial with PDB 1BJU
2017 Dock tutorial
2017 RCR GROUP MEETING
2017a DOCK tutorial
2018
2018-2019 AMS-532 Fall-Spring
2018 AMBER tutorial with 1c87
2018 AMBER tutorial with 2nnq
2018 AMS-535 Fall
2018 AMS-536 Spring
2018 DOCK tutorial 1 with PDBID 2NNQ
2018 DOCK tutorial 2 with PDBID 1C87
2018 Denovo design tutorial 1 with PDB 2NNQ
2018 Denovo design tutorial 2 with PDB 1C87
2018 RCR GROUP MEETING
2019-2020 AMS-532 Fall-Spring
2019 AMBER tutorial with PDBID 2BXF
2019 AMS-535 Fall
2019 AMS-536 Spring
2019 Covalent docking tutorial 1 with PDB 2VKG
2019 Covalent docking tutorial 1 with PDB 5VKG
2019 DOCK GA tutorial 1 with 2NNQ
2019 DOCK tutorial 1 with PDBID 2BXF
2019 DOCK tutorial 2 with PDBID 2P16
2019 DOCK tutorial 3 with PDBID 3JQZ
2019 Denovo design tutorial 1 with PDB 2BXF
2019 Denovo design tutorial 2 with PDB 2P16
2019 Denovo design tutorial 3 with PDB 3JQZ
2019 RCR GROUP MEETING
2020-2021 AMS-532 Fall-Spring
2020 AMBER tutorial with PDBID 3VJK
2020 AMS-535 Fall
2020 AMS-536 Spring
2020 AMS-536 Spring (original syllabus)
2020 AMS-536 Spring (revised syllabus)
2020 DOCK tutorial 1 with PDBID 3VJK
2020 DOCK tutorial 1 with PDBID XXXX
2020 DOCK tutorial 2 with PDBID 2GQG
2020 DOCK tutorial 2 with PDBID XXXX
2020 DOCK tutorial 3 with PDBID 4F4P
2020 DOCK tutorial 4 with PDBID 6UZW
2020 DOCK tutorial 4 with PDBID XXXX
2020 Denovo tutorial 1 with PDBID 3VJK
2020 Denovo tutorial 2 with PDBID 2GQG
2020 Denovo tutorial 3 with PDBID 4F4P
2020 Denovo tutorial 4 with PDBID 6UZW
2021-2022 AMS-532 Fall-Spring
2021 AMBER tutorial 1 with PDBID 1HW9
2021 AMBER tutorial 3 with PDBID 1S19
2021 AMS-535 Fall
2021 AMS-536 Spring
2021 DOCK tutorial 1 with PDBID 1HW9
2021 DOCK tutorial 2 with PDBID 2ZD1
2021 DOCK tutorial 3 with PDBID 1S19
2021 DOCK tutorial 4 with PDBID 1EFY
2021 Denovo tutorial 1 with PDBID 1HW9
2021 Denovo tutorial 2 with PDBID 2ZD1
2021 Denovo tutorial 3 with PDBID 1S19
2021 Denovo tutorial 4 with PDBID 1EFY
2022-2023 AMS-532 Fall-Spring
2022 AMBER tutorial 1 with PDBID 6ME2
2022 AMBER tutorial 3 with PDBID 1X70
2022 AMS-535 Fall
2022 AMS-536 Spring
2022 Covalent docking tutorial updated with PDB xxxx
2022 DOCK tutorial 1 with PDBID 6ME2
2022 DOCK tutorial 2 with PDBID 4ZUD
2022 DOCK tutorial 3 with PDBID 1X70
2022 Denovo tutorial 1 with PDBID 6ME2
2022 Denovo tutorial 2 with PDBID 4ZUD
2022 Denovo tutorial 3 with PDBID 1X70
2022 RCR GROUP MEETING
2023-2024 AMS-532 Fall-Spring
2023 AMBER tutorial 1 with PDBID 4S0V
2023 AMBER tutorial 2 with PDBID 3WZE
2023 AMBER tutorial 3 with PDBID 2P16
2023 AMS-535 Fall
2023 AMS-536 Spring
2023 DOCK tutorial 1 with PDBID 4S0V
2023 DOCK tutorial 2 with PDBID 3WZE
2023 DOCK tutorial 3 with PDBID 2P16
2023 Denovo tutorial 1 with PDBID 4S0V
2023 Denovo tutorial 2 with PDBID 3WZE
2023 Denovo tutorial 3 with PDBID 2P16
2024-2025 AMS-532 Fall-Spring
2024 AMBER tutorial 1 with PDBID 2ITO
2024 AMBER tutorial 2 with PDBID 1NDV
2024 AMBER tutorial 3 with PDBID 1Y0X
2024 AMS-535 Fall
2024 AMS-536 Spring
2024 DOCK GA tutorial 1 with 1NDV
2024 DOCK tutorial 1 with PDBID 2ITO
2024 DOCK tutorial 2 with PDBID 1NDV
2024 DOCK tutorial 3 with PDBID 1Y0X
2024 Denovo tutorial 1 with PDBID 2ITO
2024 Denovo tutorial 3 with PDBID 1Y0X
3D Analog Library Generation Using Pubchem and Zinc
AMBER Lipid Tutorials
AMBER TI Tutorials
AMBER Tutorials
AMBER tricks
AMS-531 Laboratory Rotations in Computational Biology
AMS-532: Lab Rotations/Journal Club Guidelines
AMS-532 Guidlines
AMS-532 Journal Club in Computational Biology
AMS-532 Laboratory Rotations and Journal Club in Computational Biology
AMS-535 Introduction to Computational Structural Biology and Drug Design
AMS-536 Molecular Modeling of Biological Molecules
Activating your Seawulf Account
Additional DOCK6 Information
Advanced Dock Utilities
Advanced Dock Utilities/Information
Amber on Seawulf (compilation)
Amber to mol2 (protein)
Amber to pdb
Ams.stonybrook.edu
Analog Library - Pubchem & Zinc
Analysis Tools Repository
Announcements: Fall 2013
Apply for NYBlue
Apply for cluster
Archiving old data
AutoDock4 Benchmark Results
AutoDock4 Pose Reproduction Tutorial
AutoDock Vina Benchmark Results
AutoDock Vina Pose Reproduction Tutorial
Automated Families generation from the Protein Databank
Automated Family generation from PDB
BASH scripting
BOSS Pure Liquid Simulation Notes
Benchmarking Protocols and Lab SOPs
Benchmarking Protocols and Results
Benchmarking Results
Binding Footprint Program
Blocked Standard Error of the Mean
BlueGene
CONGA
CONGA (CONstruction by Genetic Algorithm)
CONGA Parameter List
CVS Commands
C Shell Scripting
Cancer
Chimera
Cluster compilations
Clustering in R
Coming Soon
Common Errors - ctrl M
Compiling Applications for BG/L
Compiling GROMACS on Cluster
Config
Cross Docking SB2024 V1 DOCK6.10 A
DGHYD
DOCK6 POSE Reproduction
DOCK Abbreviations Guide
DOCK Benchmarking
DOCK CV Benchmarking
DOCK CV Development Goals
DOCK CV Input File(s)
DOCK CV Tutorials
DOCK Compilation
DOCK DN Benchmarking
DOCK DN Development Goals
DOCK DN Input File(s)
DOCK DN Parameters
DOCK DN Tutorials
DOCK DN Utilities
DOCK DN Utilities/Info
DOCK Denovo
DOCK Denovo Refinement
DOCK Denovo Run
DOCK GA Developer Progress
DOCK GA Development Goals
DOCK GA Input File(s)
DOCK GA Parameter List
DOCK GA Parameters
DOCK GA Tutorials
DOCK GIST Parameters
DOCK Installation
DOCK NOVA
DOCK Release Objectives
DOCK Tutorials
DOCK VS Benchmarking
DOCK VS Development Goals
DOCK VS Parameters
DOCK VS Tutorials
DOCK VS Utilities
DOCK VS Utilities/Info
Database Enrichment SB2024 V1 DOCK6.10 A
De Novo Design
De Novo Design (DOCK DN)
De Novo Design (previously NOVA)
De novo Benchmarking
De novo DOCK
De novo Developer Progress
Dell 5110cn Printer
Developer's Info Goals
Development Goals Archive
Disulfide.txt
Drug-like organic molecules
Energy Scoring Method in Grid
Ethernet Cables
Example Input Files
Example of an CONGA Input file
Example of an Ensemble Evolution Input file
Example of an Input file
Example of an Single Molecule Evolution Input file
Example scripts
Families in the Protein Databank
Flex.in
Footprint Plot Visualization
Formating your Thesis
Formatting your Thesis
Fourier fit
Fragment Library Generation
GRD-500 Integrity in Science
Gdb (GNU Debugger)
General Dock Development Goals
General Dock Utilities
General Dock Utilities/Info
Genion.mdp
Get Job ids to use for llcancel
Get time estimate for free blocks
Get time for job completion
Getting a BNL Account
Ghostscript
Gnuplot
Grid.in
HIV/AIDS
Histograms in R
How to purchase compounds for Rizzo lab
INSPH
Influenza
Installing DOCK
Installing MSMS for VMD
Integration.pl
Joe and Brian de novo stuff
Joint Group Meeting 2007-2009
Joint Group Meeting 2010
Joint Group Meeting 2011
Joint Group Meeting 2012
Joint Group Meeting 2013
Journal Articles from UCSF
Lab-designed code and programs
Lab SOP
Legacy Info
LoadLeveler Chain Jobs
MATLAB
MD Simulation: Protein in Water
MD Simulation: Protein in Water (Pt. 2)
MOE
MPICH
Main Page
Make Unique script usage
Make surface
Making images for publication
Making images for publication using vmd
Method development
NAMD Amber inputs
NAMD on Seawulf
NAMD to mol2
NAMD tutorial
NOVA
NOVA (Navigation and Optimization for Virtual Assembly)
No t4 step1 inputgen.bash

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