PPT-Secondary structure prediction

Miguel Andrade Faculty of Biology Johannes Gutenberg University Institute of Molecular Biology Mainz Germany a ndradeunimainzde Secondary structure prediction Amino acid sequence gt Secondary structure. Static Branch Prediction. Code around delayed branch. To reorder code around branches, need to predict branch statically when compile . Simplest scheme is to predict a branch as taken. Average misprediction = untaken branch frequency = 34% SPEC. 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. Elad. . Hazan. (. Technion. ). Satyen Kale . (Yahoo! Labs). Shai. . Shalev-Shwartz. (Hebrew University). Three Prediction Problems: . I. Online Collaborative Filtering. Users: . {1, 2, …, m}. Movies: . Assumptions on noise in linear regression allow us to estimate the prediction variance due to the noise at any point.. Prediction variance is usually large when you are far from a data point.. We distinguish between interpolation, when we are in the convex hull of the data points, and extrapolation where we are outside.. CS 3220. Fall 2014. Hadi Esmaeilzadeh. hadi@cc.gatech.edu. . Georgia Institute of Technology. Some slides adopted from Prof. . Milos . Prvulovic. Control Hazards Revisited. Forwarding helps a lot with data hazards. Yongin. Kwon, . Sangmin. Lee, . Hayoon. Yi, . Donghyun. Kwon, . Seungjun. Yang, . Byung. -. Gon. Chun,. Ling Huang, . Petros. . Maniatis. , . Mayur. . Naik. , . Yunheung. . Paek. USENIX ATC’13. Research Interests/Needs. 1. Outline. Operational Prediction Branch research needs. Operational Monitoring Branch research needs. New experimental products at CPC. Background on CPC. Thanks to CICS/ESSIC/UMD for Inviting us . Emura. , Chen & Chen [ 2012, . PLoS. ONE 7(10) ] . Takeshi . Emura. (NCU). Joint work with Dr. Yi-. Hau. Chen and Dr. . Hsuan. -Yu Chen (. Sinica. ). 國立東華大學 應用數學系. 1. 2013/5/17. Prediction is important for action selection. The problem:. prediction of future reward. The algorithm:. temporal difference learning. Neural implementation:. dopamine dependent learning in BG. A precise computational model of learning allows one to look in the brain for “hidden variables” postulated by the model. 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. 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.. In. . boerhaaviA (dicot) . Dracaena (monocot) . Secondary growth. Secondary growth is the growth that results from cell division in the cambia or lateral meristems and that causes the stems and roots thickning. . 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.