PPT-Protein Ligand Interactions:

A Method and its Application to Drug Discovery PHAR 201Bioinformatics I Philip E Bourne Department of Pharmacology UCSD pbourneucsdedu PHAR201 Lecture 12 2012 Todays Lecture in Context. Interface between Physics and Biology. . Shekhar. C. . Mande. Centre for DNA Fingerprinting and Diagnostics. Hyderabad. Emerging Paradigm of Modern Practice of Science. Integration of all branches of sciences (learning)…….. Interactions. June 18, 2015. Why PPI?. Protein-protein interactions determine outcome of most cellular processes. Proteins which are close homologues often interact in the same way. Protein-protein interactions place evolutionary constraints on protein sequence and structural divergence. Department of Chemistry. University of Victoria. Winter, 2013. Measurement of Binding Constants and Heats of Binding using Isothermal Titration Calorimeter. Acknowledgement. . Professor Hof. Classmates. Computer-Aided Drug Discovery. Mike Gilson. School of Pharmacy. mgilson@ucsd.edu. 2-0622. Outline. Overview of drug discovery. Structure-based computational methods. When we know the structure of the targeted protein. L. L. L. R. R. L. L. R. R. L. L. water. DOCKING SIMULATIONS. water. R. L. R. L. L. R. L. R. L. R. DOCKING SIMULATIONS. Computer-aided drug design (CADD). Known ligand(s). No known ligand. Known protein structure. Pratt & . Cornely. , Chapter 10. Terms for Signal Transduction. Ligand (first messenger). Receptor (transducer). Primary Effector. Second . messenger. Second effector, etc.. Target proteins/DNA. Ligands. Field Theory: . σ. Bonding. a. 1g. t. 1u. e. g. Combination of Metal and Ligand Orbitals in an Octahedral Complex. 2. Overlap of metal . orbitals. and linear combination of . ligand. group . orbitals. Employ rigid or flexible structures for ligand and receptor . (Side-chains or Back-bone flexible). How to handle molecular motions?. Treat with full atomic detail or simplified models?. . Which docking energy function is best?. Audry Kang. 7/15/2013. Central Dogma of Molecular Biology. Protein Review. Primary Structure: . Chain of amino acids. Secondary Structures: . Hydrogen bonds resulting in alpha helix, beta sheet and turns. June 12, 2018. Why PPI?. Protein-protein interactions determine outcome of most cellular processes. Proteins which are close homologues often interact in the same way. Protein-protein interactions place evolutionary constraints on protein sequence and structural divergence. Question. Why design novel proteins? . what can be gained by the design and characterization of novel proteins? . Can we design 3D protein structures that have never been observed?. Are the 3D structures that have not been observed in nature unattainable, or just . by Nicolas Gaeng. LSPN - Group . seminar. Lausanne, . September. 29. th. 2016. Outline. Introduction. Structure and . bonding. of chiral . sulfoxides. History. , . pioneer. . work. Preparation. of chiral . CURRENT SCIENCE, VOL. 122, NO. 2, 25 JANUARY 2022 *e-mail: vivek@vitbhopal.ac.in Department of Chemistry, School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal 466 114, India Cann and its application in . Protein-DNA/Protein  Interactions Research . and Drug Discovery. . CMSC5719. Dr. Leung, . Kwong. . Sak. Professor of Computer Science and Engineering. Mar . 26, 2012. 2. Outline.