{"content":[{"text":"Bio 5476 \n Lab Exercise \n 11.21.08 \n Instructor: Dan Kuster (d.kuster@gmail.com)","bbox":{"left":0.321078,"top":0.042758,"width":0.357858,"height":0.072295}},{"text":"Ligand Optimization and de novo design","bbox":{"left":0.246324,"top":0.152409,"width":0.5061990000000001,"height":0.031477000000000005}},{"text":"Purpose: \n Identifying a molecule that binds to a given target is often not so difficult today, with the use of sensitive high- \n throughput screens, combinatorial chemistry and abundant structural data. However, finding a specific, high- \n affinity, deliverable small molecule remains very challenging (and rewarding).","bbox":{"left":0.058824,"top":0.482152,"width":0.866823,"height":0.072295}},{"text":"In this lab you will use structure-based design tools to optimize a weak-binding lead molecule, hopefully \n generating drug-like candidates with better binding affinity.","bbox":{"left":0.058824,"top":0.569273,"width":0.8203429999999999,"height":0.037256999999999985}},{"text":"Assumptions: \n This lab assumes you are familiar with Mac OS and SYBYL. You should be comfortable with the concepts of \n conformational sampling and scoring, protein structure visualization, and ligand sketching and minimization.","bbox":{"left":0.058824,"top":0.639349,"width":0.866451,"height":0.05430200000000007}},{"text":"Lab outline: \n 0) Listen to 10 minute intro on drug design and optimization. \n 1) Launch SYBYL, set up your RACHEL demo environment. \n 2) Do the RACHEL tutorials. \n 3) Use RACHEL to optimize the drug captopril in the pocket of ACE. \n 4) Answer the questions at the end.","bbox":{"left":0.058824,"top":0.726606,"width":0.578583,"height":0.10810600000000004}},{"text":"1","bbox":{"left":0.931373,"top":0.934803,"width":0.009804000000000035,"height":0.020212000000000008}}],"images_bbox":[{"left":0.352941,"top":0.196023,"width":0.294118,"height":0.270833}],"images_bbox_not_text_overlap":[{"left":0.352941,"top":0.196023,"width":0.294118,"height":0.270833}]}