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Structural Bioinformatics

Structural Bioinformatics. R. Sowdhamini National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore, INDIA. 1. Prediction of Secondary Structure and Tertiary Interactions in Proteins. How to predict  -sheets?. Problems in prediction: Sequentially distant

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Structural Bioinformatics

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  1. Structural Bioinformatics R. Sowdhamini National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore, INDIA

  2. 1. Prediction of Secondary Structure and Tertiary Interactions in Proteins How to predict -sheets? • Problems in prediction: • Sequentially distant • interactions; • - Non-ideal nature Relevance: protein structure prediction Picture taken from Branden & Tooze book

  3. Paper in this session Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms Authors:Cheng, Baldi

  4. 2. Ab-initio prediction of protein structure How does a protein fold? YNRLCIKPRDWIDECDSNEGGERAYFRNG KGGCDSFWICPEDHTGADYYSSYRDCFNACI Picture taken from Branden & Tooze book

  5. Improving Protein Structure Prediction With Model-Based Search Paper in this session Authors: Brunette, Brock

  6. 3. Prediction of active sites of proteins Can active site residues be recognised? Problems:too many cavities in structures! Limitations:paucity of sequence homologues Relevance in Structural Genomics initiative Picture taken from Sowdhamini’s lab

  7. Prediction of Active Sites for Protein Structures from Computed Chemical Properties Paper in this session Authors: Ko, Murga, Ondrechen

  8. 4. Prediction of functionally important regions in proteins Can functionally important residues be recognised? Can structure prediction lead to function prediction? Picture taken from Sowdhamini’s lab

  9. In silico Identification of Functional Regions in Proteins Paper in this session Authors: Nimrod, Glaser, Steinberg, Ben-Tal, Pupko

  10. 5. Objective measurement of evolutionary timescales of protein folds Can the age of a protein fold be determined? Limitations:accurate Descriptor of age of fold; Limited number of data Relevance to protein Fold evolution Picture taken from Mark Gernstein’s Lab Web page

  11. How Old is Your Fold? Paper in this session Authors:Winstanley, Abeln, Deane

  12. 6. Prediction of folding nuclei in proteins Can residues that initiate folding in a protein be recognised? Limitations:absence of accurate energy functions; Dependence on availability df sequence homologues Relevance: biophysics of Protein unfolding/folding events Picture taken from Jayant Udgaonkar’s Lab Web page

  13. Search for Folding Nuclei in Native Protein Structures Paper in this session Authors:Shmygelska

  14. 7. Prediction of conformational changes in proteins How to simulate changes in flexible parts of proteins? Limitations:accurate Description of energy Functions; Macromolecular nature Relevance to biological processes Picture taken from Mark Gernstein’s Lab Web page

  15. A Path Planning Approach for Computing Large-Amplitude Motions of Flexible Molecules Paper in this session Authors: Cortes, Simeon, Ruiz de Angulo, Guieysse, Remaud-Simeon, Tran

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