Simulation-Based Drug Discovery

National Biomedical Computation Resource (NBCR) and the Theoretical and Computational Biophysics Group (TCBG) are pleased to offer a joint workshop on the theme of Molecular Simulation and Small Molecule Drug Discovery. This week-long intensive program will introduce 12-25 students to principles, methods, and NBCR / TCBG tools for simulating receptors (globular and membrane bound), small molecule docking, rigorous free energy calculations, and drug discovery strategies and workflows.

In consultation with the course organizers, those accepted into the program will be encouraged to bring and work with their own drug targets. Workshop slots are limited and available on a first-come, first-serve basis; deadline for applications is August 1, 2015. Women and underrepresented students are strongly encouraged to apply.

Dates: September 21-25, 2015
Venue: University of California San Diego, La Jolla, CA, USA
Organizers: Rommie Amaro

Instructors Contact
Art Olson Michel Sanner
Victoria Feher Robert Swift
Emad Tajkhorshid Abhishek Singha Roy
Chris Chipot Yinglong Miao
Rommie Amaro Dora Warshaviak
Ilkay Altintas  
Registration questions Teri Simas This email address is being protected from spambots. You need JavaScript enabled to view it.
Workshop questions Teri Simas This email address is being protected from spambots. You need JavaScript enabled to view it.

Please see tentative day-by day schedule: Day 1 | Day 2 | Day 3 | Day 4 | Day 5

Registration Info Registration for the workshop is now open – please register using https://www.regonline.com/NBCR-SBDD-2015

Monday, September 21, 2015

AM: Docking small molecules
Instructors: Art Olson, Michel Sanner, The Scripps Research Institute

PM: Identifying flexible pockets and neural network scoring methods (POVME and NNScore)
Instructors: Jacob Durrant, Lane Votapka

Tuesday, September 22, 2015

Developing target focused libraries, hot spot mapping, and virtual screening strategies

Instructors: Victoria Feher, Robert Swift, University of California, San Diego
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
09:00 - 10:30 The Goldilocks method to structure-based virtual screening - selecting the "just right"
target-focused library
L
10:30 - 10:45 Coffee Break
10:45 - 11:30 Training Structure-based ensembles for docking profit L
11:30 - 12:00 Hands-on H
12:00 - 13:30 Lunch
13:30 - 14:30 Identifying drugable pockets for protein ensembles (FTMap and FTProd) L
14:30 - 14:45 Coffee Break
14:45 - 17:00 Identifying drugable pockets for protein ensembles (FTMap and FTProd) H 

Wednesday, September 23, 2015

VMD, NAMD, simulating membrane proteins, MDFF

Instructors: Emad Tajkhorshid and Abhishek Singha Roy, University of Illinois at Urbana-Champaign
Instruction type: L = Lecture, H = Hands on Tutorial

Time Track Type
09:00 - 10:30 Introduction to VMD and NAMD L
10:30 - 10:45 Coffee Break
10:45 - 12:00 Membraine simulations with NAMD L
12:00 - 13:30 Lunch
13:30 - 14:30 Molecular dynamics flexible fitting (part 1) L
14:30 - 14:45 Coffee Break
14:45 - 17:00 Hands-on H

Thursday, September 24, 2015

Free Energy Methods, MDFF

Instructors: Chris Chipot and Abhishek Singha Roy, University of Illinois at Urbana-Champaign
Instruction type: L = Lecture, H = Hands on Tutorial

Time Track Type
09:00 - 10:30 Introduction to free-energy calculations (part 1) L
10:30 - 10:45 Coffee Break
10:45 - 12:00 Introduction to free-energy calculations (part 2) L
12:00 - 13:30 Lunch
13:30 - 14:30 Molecular dynamics flexible fitting (part 2) L
14:30 - 14:45 Group Photo
14:45 - 17:00 Hands-on H

Friday, September 25, 2015

AM: Gaussian Accelerated Molecular Dynamics Simulations
Instructors: Yinglong Miao

PM: Covalent Docking with Schrödinger Tools
Instructors: Dora Warshaviak, Schrodinger
Instruction type: L = Lecture, H= Hands on Tutorial

Time Track Type
09:00 - 10:00 Unconstrained enhanced sampling of biomolecules L
10:00 - 10:15 Coffee Break
10:15 - 12:00 Hands-on H
12:00 - 13:30 Lunch
13:30 - 13:45 Workshop evaluations
13:45 - 14:45 CovDock (part 1) L
14:45 - 15:00 Coffee Break
15:00 - 16:00 CovDock (part 2) L
16:00 - 17:00 Closing remarks

The materials for this workshop, including videos of the lectures and tutorials, are available through the Biomedical Big Data Training Collaborative.

Those with accounts on the site can directly access the course via this link.

Wireless
Please use UCSD-GUESTnetwork for your wireless connection:

Login

Some sessions require users to login to the cluster. Each participant of such sessions is given an account. All participants were sent an email asking to send a public ssh2 key and a confirmation email with the user account was send after receiving a key. The account name is of the form sbddXX.

To login to your account on the cluster please follow these steps:

  • MacOS / Linux
    1. open a terminal or an Xterm window
    2. ssh This email address is being protected from spambots. You need JavaScript enabled to view it.
      and give your passphrase (used for ssh key generation) when prompted.
    NOTE: The ssh command assumes a default ssh key name (id_dsa or Id_rsa) and location (in ~/.ssh/ directory). If you created your key with a different name or in a different location from a default, you will need to pass that name with -i flag.
    For example, you have created a key and saved it with the name myKey. In your ~/.ssh/ directory there will be 2 files: myKey file (private key) and myKey.pub file (public key). You have sent the public portion of the key (~/.ssh/myKey.pub file) to This email address is being protected from spambots. You need JavaScript enabled to view it.. To login to the cluster you will need to:
    ssh This email address is being protected from spambots. You need JavaScript enabled to view it. -i ~/.ssh/myKey
  • Windows 7
    1. open PuTTY and enter host name kivid.ucsd.edu
    2. in Conneciton->SSH menu choose Auth and browse for your key
    3. click Open
    4. in the new opened window login with the acount name given to you
    5. when prompted, give your passphrase

Follow these instructions only if you are attending Day 5 morning session.

Prerequisites:

  • Familiarity with UNIX is highly recommended, including basic scripting.
  • You will need VNC viewer installed on your laptop. Free options:

VNC setup

Each student is assigned an account, a VNC connection password and a compute node to connect to. Conventions:

  • account: sbddXX - 4 letters followed by 2 digits
  • password: WORD, instructor will give you a WORD

Sequence of commands to use VNC connection from your laptop to the cluster during the tutorial.

  1. On your laptop: open an ssh tunnel to the cluster as
    ssh -L 5920:compute-0-1:59XX kivid.ucsd.edu -l sbddXX
    Provide correct values for XX which is a numeric part of your account. Type your ssh key passphrase when prompted
  2. On the cluster: Once you login, start the vncserver by executing
    /share/apps/bin/startVNC
    You will see the output similar to:
    Using display :12 for vnc
    Warning: untrusted X11 forwarding setup failed: xauth key data not generated
    Warning: No xauth data; using fake authentication data for X11 forwarding.
    New 'compute-0-1.local:12 (sbdd12)' desktop is compute-0-1.local:12
    Starting applications specified in /home/sbdd12/.vnc/xstartup
    Log file is /home/sbdd12/.vnc/compute-0-1.local:12.log
  3. On your laptop: use your installed VNC client and open a new connection window:
    In the new window type the information requested for:
    • for VNC Server: localhost:5920
    • for Encryption: (leave Let VNC Server choose)
    Click on Connect button.

     On the next popup window click Continue

     then in the VNC Viewer window type your password (given by instructor) and click ok.



     If you are successful a cluster Desktop window will appear. From Applications -> System Tools menus choose Terminal to open the terminal window and you will be able to start your visualization work.
  4. After you finish your work
    1. On your laptop: close the cluster Desktop window
    2. On the cluster:
      /share/apps/bin/stopVNC
      exit