All articles
- 01mi.in
- 04md.in
- 2006-2007 AMS-532 Fall-Spring
- 2007-2006 AMS-532 Fall-Spring
- 2007-2008 AMS-532 Fall-Spring
- 2007-2009
- 2008-2007 AMS-532 Fall-Spring
- 2008-2009
- 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
- 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 DOCK tutorial with Thrombin
- 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 DOCK tutorial 3 with PDBID 5UPG
- 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
- AMBER tutorial
- AMBER tutorial with Trpcage
- 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-532 Laboratory Rotations and Journal Club in Computational Structural Biology
- AMS-535 Introduction to Computational Structural Biology and Drug Design
- AMS-536 Molecular Modeling of Biological Molecules
- AMS 532: Lab Rotations/Journal Club Guidelines
- 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
- BOSS Pure Liquid Simulation Notes
- BOSS pure liquid simulation
- Benchmarking
- Benchmarking Lab SOP and Results
- Benchmarking Lab SOPs
- Benchmarking Protocols and Lab SOPs
- Benchmarking Protocols and Results
- Benchmarking Results
- Benchmarking Tutorials & Lab SOPs
- Benchmarking Tutorials and Lab SOPs
- Binding Footprint Program
- Blocked Standard Error of the Mean
- BlueGene
- BlueGene LoadLeveler Jobs with Multiple Steps (Chain Jobs)
- 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
- 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 Tutorial with 1LAH
- DOCK Tutorials
- DOCK VS Benchmarking
- DOCK VS Development Goals
- DOCK VS Parameters
- DOCK VS Tutorials
- DOCK VS Utilities
- DOCK VS Utilities/Info
- DOCK tutorial
- DOCK tutorial with 1LAH
- DOCK tutorial with Gleevec
- DOCK tutorial with neuraminidase
- Database Enrichment
- 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
- Free Energy of Hydration Test-set
- 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
- Hello World
- Histograms in R
- How to purchase compounds for Rizzo lab
- INSPH
- Influenza
- Input for md
- Input for min
- Installing DOCK
- Installing MSMS for VMD