PPT-Structure Databases: The Protein Data Bank

Swanand Gore amp Gerard Kleywegt PDBe EBI May 7 th 2010 910 am Macromolecular Crystallography Course Outline Structural Biology and Bioinformatics Databases in Structural Bioinformatics. 1. Assignment #1. Think about what you have learned about molecular structure not just from a purely scientific perspective, but from a conceptual perspective. What concepts and associated relationships would you need to capture to create a database or data structure to retrieve data on . What can we compare?. 3D shapes (RMSD). Atomic motions (B-value, RMSF). Solvent accessibilities (SASA). AMIGOS - Reads an RNA PDB file and outputs a complete table of torsion angle calculations.. APBS - Software for evaluating the electrostatic properties of . & . DATA WAREHOUSES. Access. to a Gold Mine of Information. “The. . real value. . will come from getting the. . right information. . to the. . right people. , at the. . right time. , and giving those people the. C483 Spring 2013. 1. Which . statement is false about a globular protein that performs its biological function as a single independent polypeptide chain?. A. ) Its tertiary structure is likely stabilized by the interactions of amino acid side chains . Gustavo Caetano - . Anolles. 1. PowerPoint by Casey . Hanson. Protein Sequence, Structure, and Function | Gustavo Caetano - Anolles | 2015. Exercise. In this exercise we will be doing the following:. The Protein Data Bank. Swanand. Gore & Gerard . Kleywegt. PDBe. – EBI. May 7. th. 2010, 9-10 am. Macromolecular Crystallography Course. Outline. Structural Biology and Bioinformatics. Databases in Structural Bioinformatics. Avdesh Mishra, . Md. . Tamjidul. . Hoque. {amishra2, . thoque. }@uno.edu. Presented By: Avdesh Mishra. Department of Computer Science. Protein structure in its native state gains lowest free energy. 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 . (1979) –. Bio-. biology,Informatique. -Data processing. Study of information content and flow in a biological system with the help of IT.. Multidisciplinary branch. Historical background:. 1961-identified mRNA- . UNIT IV. DATABASE. A database is a . computarised. library used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria.. The development of databases to handle the vast amount of molecular biological data is a fundamental task of bioinformatics.. Program for today:. - . Structures. . from. . p. rotein. X-. ray. . crystallography. - . Statistics. . of. . protein. . structures. - Statistical . potentials. 1. V10. Processing of Biological Data. 1 REGULATIONS AND SYLLABI (Effective from 2019 - 2020 ) Centre for Bioinformatics SCHOOL OF LIFE SCIENCES PONDICHERRY UNIVERSITY PUDUCHERRY 2 Pondicherry University School of Life Sciences Centre for 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.. era. The rise of bioinformatics. An information explosion!. Bioinformatics. Computational tools are developed to collect, organize and analyze a wide variety of biological data. Advances in DNA sequencing technologies have accelerated the pace of discovery. Much of the process is now automated. .