Difference between revisions of "2023 AMS-535 Fall"

Latest revision as of 13:10, 26 November 2023

Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage

GENERAL INFORMATION: AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.

Learning Objectives

• (1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods.
• (2) Dissect seminal theory and application papers relevant to computational drug design.
• (3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design.
• (4) Read, participate in discussion, and be tested across five key subject areas:
  • (i) Drug Discovery and Biomolecular Structure:
    Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids
    Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure
  • (ii) Molecular Modeling:
    Classical Force Fields (Molecular Mechanics),
    Solvent Models, Condensed-phase Calculations, Parameter Development
  • (iii) Sampling Methods:
    Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC)
    Sampling Techniques, Predicting Protein Structure, Protein Folding
  • (iv) Lead Discovery:
    Docking as a Lead Generation Tool, Docking Algorithms
    Discovery Methods I, Discovery Methods II, Applications
  • (v) Lead Refinement:
    Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)
    MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction

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.

Syllabus Notes

This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:

General Information:

• We will hold class at the regularly scheduled time (M/W 2:30-3:50PM) and class will be held in person. There is no online section.
• The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.
• All class correspondence should be addressed to ALL course Instructors.

Discussion Sessions:

• The bulk of the classes will be devoted to in-person discussion, in breakout groups, facilitated by an assigned discussion leader. Papers will be read prior to meeting (1-2 per class) for which everyone will also have watched an oral presentation on the paper (1-2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class.
• For each paper discussed, one (1) student in each discussion group will be assigned as discussion leader. The discussion group leader will be expected to understand and guide discussion on the paper. If there is any confusion regarding paper content as a discussion leader, students should reach out to TAs well before the class in which they are to lead.
• The Instructors(s) will moderate and participate in discussion, as well as field questions and clear up any misunderstandings, and take over discussion when necessary.
• For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. Copies of these questions will be handed to the instructors prior to the beginning of discussion.
• A sizeable portion of the class grade (30%) is based on these discussion sections. Thus, it is important that everyone attend all of the classes and participate in each discussion to receive full credit.
• If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page Paper Summary Sheet answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
• If a student misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.

Oral Presentations:

• Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below.
• Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.
• Course participants will watch the student presentations and, independently, read the paper before the class in which they are to be discussed.
• Course participants will score each student presentation using a Presentation Assessment Sheet which will be emailed to ALL Instructors within 24 hours after the class in which the presentation was discussed.

In-class Quizzes:

• Five quizzes will be used to assess student understanding of the course material.
• The quiz format is in-class, closed book.
• Answers to quiz questions should integrate topics, concepts, and outcomes of the different papers covered for the section being tested.
• Students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary.

Recording Your Oral Presentations 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 paper 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 20-25 minutes)
• Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )

Oral Presentation Guidelines: Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:

• Introduction/Background (include biological relevance if applicable)
• Specifics of the System or General Problem
• Computational Methods (theory) and Details (system setup) being used
• Results and Discussion (critical interpretation of results and any problems/challenges)
• Conclusions/Future
• Acknowledgments

Class Schedule

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 Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php