2021 AMS-536 Spring
Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching)
| Instructor | Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu] |
| Teaching Assistant | Steve Pak [631-632-8519, steven dot pak - at - stonybrook dot edu] |
| Teaching Assistant | John Bickel [631-632-8519, john dot bickel - at - stonybrook dot edu] |
| Course No. | AMS-536 / CHE-536 |
| Location/Time | Online, Monday and Wednesday 2:40PM - 4:00PM |
| Office Hours | Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics |
| Acknowledgments | The AMS-536 instructors would like to thank: (1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses |
| Grading | Grades will be based on the quality of: (1) attendance, participation in class discussion, wiki tutorial construction, assisting others (25%) |
Revised Syllabus Notes
As a result of the COVID-19 outbreak the course syllabus has been revised per University guidelines to address the semester being shortened by one week and document changes necessary to teach the course online for the rest of the semester. A brief summary of the changes include:
(0) The course grading criteria has been modified (see grading breakdown above).
(1) The schedule has been revised starting March 23 2020.
(2) We will continue to hold class at the regularly scheduled time however this will now be done online via the Zoom program ( https://it.stonybrook.edu/services/zoom ).
(3) AMBER tutorials are being prerecorded by the Instructors and will be uploaded as appropriate into the course schedule as online videos.
(4) AMBER tutorials should be viewed online before each relevant Zoom meetings so that meeting time can be spent troubleshooting and providing other guidance as necessary for class tutorials.
(5) Class time normally devoted to watching and evaluating Oral Presentations will instead be used for Zoom meetings devoted to troubleshooting and providing other guidance as necessary for Class Projects.
(6) Oral Presentations of Class Projects will be recorded by each participant individually (see Recording Your Oral Presentation Using Zoom section below), at home, and then emailed to the Instructors (see Video Presentation due date below).
(7) Oral Presentations of Class Projects will be evaluated by 3 course participants and a Presentation Assessment Sheet for each talk evaluated will be submitted based on the Reviewer Assignments outlined below.
(8) The Student Accessibility Support Center Statement (see below) has been updated
(9) A Faculty Technical Support Statement (see below) has been added
Project Information
Student Project Proposal OHARE Sheet
Oral Presentation Guidelines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be between 20 and 30 minutes long. The purpose of your talks is for you to clearly and concisely present your overall progress to date including appropriate background material and interpretation of your results. Check our guidelines on how not to make a presentation. Talks should be arranged in the following order:
- Introduction/Background (include biological relevance)
- Specifics of Your System
- Computational Details (theory)
- Computational Details (system setup)
- Results and Discussion (include a critical interpretation of your results)
- Conclusions
- Future
- Acknowledgments
Recording Your Oral Presentation Using Zoom: It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:
- Download the Zoom app ( https://it.stonybrook.edu/services/zoom )
- Open the Zoom app
- Create a new Zoom meeting with only yourself (make sure audio and video are turned on)
- Share your screen
- Open your presentation in PPT and put in presentation mode
- Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)
- Stop recording and quit the meeting
- Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good
- Follow the above steps to create your "full-length" video presentation (videos should not exceed 20 minutes)
- Email your video to the Instructors who will make it available to the class (please name your Zoom video Lastname.mp4)
Final Written Report Guidelines and Example Final Papers: Written project guidelines and example papers to use as a guide are provided below.
Tutorials, Software Links, and Other Relevant Class Information
- Rizzo_Lab_Information_and_Tutorials
- Cheat Sheet:
- Unix Command Guide
- Seawulf Queue Info
- Wikitext Cheat Sheet (for preparing tutorial Wiki page)
- Wikitext Formatting Tips (for making the tutorial Wiki page pretty)
- Chimera Basics - Video
- Chimera Structure Analysis - Video
- Top Pharmaceutical Posters
- DOCK6.9 User Manual
- AMBER 16 User Manual
- Free Energy Calculations
Schedule
- Please note that a doctor's excuse will be required if you miss your scheduled oral presentation date because of illness.
| Date | Participant | Notes |
| - | SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS | Please make sure that the Zoom program is up and running on your home computer prior to the first class https://it.stonybrook.edu/services/zoom |
| 2021.02.01 Mon | Group Study | First Day of Class Seawulf accounts setup unix / vim / csh introduction Discuss presentations and final projects (OHARE sheets) |
| 2021.02.03 Wed | Group Study | Seawulf accounts setup unix / vim / csh introduction Visualization demo's Chimera and VMD |
| 2021.02.08 Mon | Group Study | Seawulf accounts setup unix / vim / csh introduction Visualization demo's Chimera and VMD |
| 2021.02.10 Wed | Group Study | Seawulf accounts setup unix / vim / csh introduction Visualization demo's Chimera and VMD |
| 2021.02.15 Mon | Group Study | Seawulf queuing system |
| 2021.02.17 Wed | Group Study | Seawulf queuing system Ethics in Writing (Rob) |
| - | SECTION 2: DOCK TUTORIAL | see Joe Allen DOCK slides |
| 2021.02.22 Mon | Group Study | Draft Student Project Proposal OHARE Sheet Due Tutorials: DOCK virtual screening individual project discussion |
| 2021.02.24 Wed | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2021.03.01 Mon | Group Study | Final Student Project Proposal OHARE Sheet Due Tutorials: DOCK virtual screening individual project discussion |
| 2021.03.03 Wed | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2021.03.08 Mon | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2021.03.10 Wed | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2021.03.15 Mon | Group Study | Tutorials: DOCK de novo design individual project discussion |
| 2021.03.17 Wed | Group Study | Tutorials: DOCK de novo design individual project discussion |
| - | SECTION 3: AMBER TUTORIAL | see Lingling Jiang AMBER slides |
| 2021.03.22 Mon | Group Study | Tutorials: AMBER molecular dynamics individual project discussion |
| 2021.03.24 Wed | Group Study | Tutorials: AMBER molecular dynamics individual project discussion |
| 2021.03.29 Mon | Group Study | Tutorials: AMBER molecular dynamics individual project discussion |
| 2021.03.31 Wed | Group Study | Tutorials: AMBER molecular dynamics individual project discussion |
| 2021.04.05 Mon | Group Study | Tutorials: AMBER molecular dynamics individual project discussion |
| 2021.04.07 Wed | Group Study | Tutorials: AMBER molecular dynamics individual project discussion |
| - | SECTION 4: CLASS PROJECTS | |
| 2021.04.12 Mon | Group Study | Draft Paper Due Project Analysis/Troubleshooting |
| 2021.04.14 Wed | Group Study | Project Analysis/Troubleshooting |
| 2021.04.19 Mon | Group Study | Project Analysis/Troubleshooting |
| 2021.04.21 Wed | Group Study | Project Analysis/Troubleshooting |
| 2021.04.26 Mon | Group Study |
Class Project Videos Due (email videos to Steve Pak by 2:30PM today, please name files Lastname.mp4)
|
| 2021.04.28 Wed | Group Study | Project Analysis/Troubleshooting |
| 2021.05.03 Mon | Group Study | Presentation Assessment Sheets Must Be Emailed to Steve Pak by 2:30PM based on your Reviewer Assignments from above Project Analysis/Troubleshooting |
| 2021.05.05 Wed | Group Study | Last Day Class Project Analysis/Troubleshooting |
| 2021.05.07 Fri | Final Written Report due by 5PM today. | Final Written Report due by 5PM today. Please email electronic copy to rizzorc -at- gmail dot com and steven dot pak - at - stonybrook dot eduu |
GENERAL INFORMATION: AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Grades will be based on the quality of the talks, participation in class discussion, attendance, and the final written report. Familiarity with working in a Unix (Linux) environment is desirable.
Learning Obectives:
- (1) Gain hands-on experience modeling biological molecules at the atomic level.
- (2) Learn to navigate linx/unix operating system
- (3) Learn shell scripting and text-based editing (vim program)
- (4) Learn to use a linux-based computing cluster that has a queuing system
- (5) Learn to use visualization software (Chimera, MOE, and VMD programs)
- (6) Setup, execute, and analyze docking (DOCK) and molecular dynamics (AMBER) tutorials.
- (7) Give oral presentations on individual research projects which includes:
- (i) Introduction/Background (include biological relevance)
- (ii) Specifics of Your System
- (iii) Computational Details (theory)
- (iv) Computational Details (system setup)
- (v) Results and Discussion (include a critical interpretation of your results)
- (vi) Conclusions
- (vii) Future
- (viii) Acknowledgments
- (8) Write a polished well-referenced manuscript in the format of a peer-reviewed Journal Article.
LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.
PRESENTATION DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.
Required Syllabi Statements:
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php
Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.
Academic Integrity Statement: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html
Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.
