電腦模擬運算之藥物設計
Computational Chemistry Related to Drug Design
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1 08:00–08:50 | 電腦模擬運算之藥物設計 2 節連堂 |
2 09:00–09:50 |
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This course will provide hands-on experience with modern computational methods used in the drug design process. A variety of different computational methods will be described and applied using real-life drugs and related molecules. Instructor: Prof. Dean Tantillo; djtantillo@ucdavis.edu TA: Ian Torrence; istorrence@ucdavis.edu Course Overview Lab 1: Visualizing and Interacting with Protein Structures Lab 2: Structural Conservation in Proteins Lab 3: Geometry optimization of small molecules Lab 4: Property screen of small molecule library Lab 5: Ligand based virtual screen Lab 6: Docking lead molecule into a protein’s active site Lab 7: Design of Bioisosteres
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Policies • assignments: All late assignments will be assessed a penalty that is proportional to how late the assignment is. No exceptions will be made. • mutual respect: We are all adults and should treat each other as such. Cheating of any kind (including plagiarism!) will not be tolerated. Strategies for Success • don’t wait: The drug design project is a lot of work, so start as early as possible!
Course Requirements Mini lab reports: 450 points (50 – 95 each) Drug Design Project: 550 points (3 parts) Total: 1000 points Drug Design Project Directions for each can be found in the Lab Manual • Proposal: your choice of a “drug family”; 25 points • Literature Report: background on your “drug family” (~5 pages); your choice of a “drug family”; 100 points • Presentation: brief presentation to the class on your “drug family” and designs; 75 points • Final Project: computations and report on your “drug family”; 350 points Examples of “A” level final projects: https://www.biorxiv.org/content/10.1101/772137v1.full.pdf https://www.biorxiv.org/content/10.1101/2023.02.25.529947v1.full https://www.biorxiv.org/content/10.1101/2022.04.06.487400v1.full https://www.biorxiv.org/content/10.1101/2022.04.27.489637v1.full https://www.biorxiv.org/content/10.1101/2022.10.10.511679v1.full • Citations: All citation has to be done ACS style (please visit see ACS_cittation.pdf to see how you cite). Must also include in-text citation. An example of writing with in-text style citation can be found here: https://www.biorxiv.org/content/10.1101/772137v1.full.pdf
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Recommended Texts • “Molecules and Medicine” E. J. Corey, Barbara Czako, Laszlo Kurti Wiley, 2007 • “The Organic Chemistry of Drug Design and Drug Action”, Richard B. Silverman Elsevier/Academic Press Our Expectations • This course is not about memorization. It is about developing analytical thinking and problemsolving skills. • We will utilize and expand upon undergraduate Organic Chemistry.
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