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 | ||||||||||||||||
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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:
- MacOS / Linux Using wireless as a guest at UCSD
- WIndows Accessing UCSD-guest wireless from Windows 7
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
- open a terminal or an Xterm window
- 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.
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
- open PuTTY and enter host name kivid.ucsd.edu
- in Conneciton->SSH menu choose Auth and browse for your key
- click Open
- in the new opened window login with the acount name given to you
- 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:
- MacOS/Linux/Windows Real VNC Viewer
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.
- 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 - 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 - 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)
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.
- After you finish your work
- On your laptop: close the cluster Desktop window
- On the cluster:
/share/apps/bin/stopVNC
exit