PPT-RNA Secondary Structure Prediction

BMICS 776 wwwbiostatwiscedubmi776 Spring 2018 Anthony Gitter gitterbiostatwiscedu These slides excluding thirdparty material are licensed under CC BYNC 40 by Mark Craven Colin Dewey and Anthony Gitter. Why do we want to know protein structure?. Classification. Functional Prediction. What is protein structure?. Primary - chains of amino acids. Secondary - interaction between groups of amino acids. Tertiary - the organization in three dimensions of all the atoms in a polypeptide. E – Recall the different structures of proteins and the test for proteins..  . C. . – Describe how a peptide bond is formed. . Describe the different structure of proteins.  . A – . Explain how the structures of a polypeptide build up and how changes to this may affect function. Yann. . Ponty. (VARNA), CNRS/. Ecole. . Polytechnique. , France. Jim Procter . (. JalView. ), University of Dundee, UK. Goals. To help your . survive. . the . RNA data jungle. .. To conceptually and . Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. X-ray crystallography . (103,988 . in PDB). need crystals. loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. loops (coil). Bovine . carboxypeptidase. A. Figure 6-28. Tertiary . structures . may contain . common patterns, or motifs, of secondary structures (= . supersecondary. structures) . βαβ. β. -hairpins. based on physicochemical . and structure descriptors. Matteo Lo Monte, . Ph.D. . 7. th . International Conference of Bioinformatics. October 2016, the . 24. th. -26. th. Rome. www.ADPr. edict. .net. VBC-603. P.G.. 30.12.2020. Protein . Strucuture. Sequence, Structure and Function. What determines fold?. Anfinsen’s experiments in 1957 demonstrated that proteins can fold spontaneously into their native conformations under physiological conditions. This implies that primary structure does indeed determine folding or 3-D . . Miguel . Andrade. Faculty of Biology, . Johannes Gutenberg University . Institute of Molecular Biology. Mainz, Germany. a. ndrade@uni-mainz.de. Secondary structure prediction. Amino acid sequence -> Secondary structure. 02 - 710 Computational Genomics Seyoung Kim Outline • RNA folding • Dynamic programming for RNA secondary structure prediction • Covariance model for RNA structure prediction RNA Basics • RN Proteins are biopolymers, made of the 20 L- . α. -amino acids linked by peptide bonds.. Polypeptide backbone is a repeating sequence of. . N-C-C-N-C-C…. The side chain or R group is not a part of the backbone or the peptide bond.. Some of the slides are adapted from Dr. Dong Xu’s lecture notes. Why secondary structure prediction?. Accurate secondary structure prediction can be an important information for the tertiary structure prediction. , . Brent O. . Cezairliyan. , Robert A. Grant, Jesse C. . Cochrane, . and Robert T. . Sauer - . Department . of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 . Presented by . Gayathri Priya Ravichandran. 1. The Gutell . Lab @ The . University of Texas at . Austin. Major Topics. Importance of RNA in the Cell. Major Changes in Paradigms. . Grand Challenges in Biology. Identification and Characterization of RNA Structure.