PPT-Improved Protein Structure Prediction using Advanced Scorin

Avdesh Mishra Md Tamjidul Hoque amishra2 thoque unoedu Presented By Avdesh Mishra Department of Computer Science Protein structure in its native state gains lowest free energy. 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. SUMI SINGH. (sxs5729). Levels of Protein Structure. 2. Thanks to: Frank . Lloyd . Wright for graphics. WOOD, BRICK etc. . . material/building blocks . AMINO ACIDS. *****************************************************************. CMPS 561-FALL 2014. SUMI SINGH. SXS5729. Protein Structure . 2. RPDFCLEPPYAGACRARIIRYFYNAKAGLCQ. Primary Structure. Sequence of Amino Acids. . Not . enough for functional prediction.. Tertiary Structure. Alexey Onufriev, . Virginia Tech. www.cs.vt.edu/~onufriev. Proteins play key roles in a living system. Three (out of many many) examples of protein functions. Catalysis:. Almost all chemical reactions in a living cell are catalyzed by protein enzymes.. Presentation to AMS Board on Enterprise Communications. September 2012. ESPC Overview. Introduction. ESPC is an . interagency collaboration . between DoD (Navy, Air Force), NOAA, DoE, NASA, and NSF for coordination of research to operations for an earth system analysis and extended range prediction capability. . and Secondary Levels. The . secondary structure . of a protein describes the structure that forms when amino acids form hydrogen bonds between the atoms in the backbone and atoms on the same or another peptide chain.. 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. Contains . carbon, hydrogen. , oxygen, and nitrogen. Remember carbohydrates and lipids contain carbon, hydrogen, and oxygen – SO protein adds . nitrogen. Some proteins also contain sulfur, iron. , copper, phosphorus, or . Jong-yeon Park, Charles A. Stock, John P. Dunne, . Xiaosong. Yang, Anthony Rosati, Jasmin G. John, . Shaoqing. Zhang. NOAA-GFDL / Princeton University. (Biogeochemistry, Ecosystems, and Climate Group). VBC-603. P.G.. 02.01.2021. Knowledge Based Approaches. Homology Modelling. Need homologues of known protein structure. Backbone modelling. Side chain modelling . Fail in absence of homology. Threading Based Methods. Dr. . Shaimaa. . Munther. . Learning Outcomes - Proteins. Define the levels of protein conformation and to indicate the role of weak interactions.. Illustrate how protein structure relates to protein function using examples.. 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.. Prediction . Wang Yang. 2014.1.3. Outline. Molecular. . Co-evolution . phenomenon. A. pplications . of Co-evolution . in . protein structure prediction and PPI prediction.. Co-evolution measurement: . Secondary structures. Tertiary structures. MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE. helices. strands. loops. Three dimensional packing of secondary structures. Protein Structures. Protein structures.