Similarity -Dissimilarity Tutorial

SIMILARITY – DISSIMILARITY COMPARISON STRUCTURAL FINGERPRINTS TUTORIAL Authors: William J. Welsh, Ph.D. Vladyslav Kholodovych, Ph.D. University of Medicine & Dentistry of New Jersey Robert Wood Johnson Medical School 675 Hoes Lane Piscataway, NJ 08854 U.S.A. (732) 235-3229 phone -3475 FAX kholodvl@umdnj.edu http://www2.umdnj.edu/~kholodvl UMDNJ Fundamentals of Bioinformatics SIMILARITY – DISSIMILARITY COMPARISON STRUCTURAL FINGERPRINTS TUTORIAL Dr. William J. Welsh, welshwj@umdnj.edu and Dr. Vladyslav Kholodovych kholodvl@umdnj.edu The following exercise will use MOE to calculate the structural fingerprints for a database of compounds using the MACCS Structural Keys, to calculate their similarity using the Tanimoto Coefficient, and then to sort them into separate clusters based on their similarity-dissimilarity. Instructions 1. Create New Directory (e.g., Similarity) 2. Download the following four files from www2.umdnj.edu/~kholodvl: Database ER.mdb; and queries q1; q2; q3. 3. Start MOE 4. Open the database called ER.mdb in the MOE Database Viewer. This database contains 49 steroidal and non-steroidal compounds (ligands) that are known to exhibit binding affinity for the estrogen receptor. In MOE, it might be interesting to visualize and compare these compare on the screen. 5. In Database Viewer, select: Compute->Fingerprints (a window will open); Select “FP ...