l02 - 6.581J / 20.482J Foundations of Algorithms and...

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6.581J / 20.482J Foundations of Algorithms and Computational Techniques in Systems Biology Professor Bruce Tidor Professor Jacob K. White 9 February 2006 MIT 6.581/ 20 .482 J F OUNDATIONS OF A LGORITHMS AND C OMPUTATIONAL Thursday T ECHNIQUES IN S YSTEMS B IOLOGY Spring 2006 L ECTURE 2 : M ODELS OF P ROTEINS ? selection of selection of problems & methods, phrasings algorithms, & techniques B IOLOGY C OMPUTATION Fundamental role of models: Understanding DNA - mRNA - Protein Prediction (genome) Design side chain i i i + 1 backbone – 1 amino acid residue H R i – 1 H O H R i + 1 C a C N C C a N N C C a H O R i H H O The “ R i ” groups are chosen from the common 20 amino acid side chains - chemical diversity (1) size: small - large N H R Gly : –H R Trp (2) polarity: hydrophobic - polar - charged O NH 2 - R Asn : C N R Leu : - R Arg : + NH 2 H NH 2 (3) uniformity of character (4) local backbone flexibility Gly - Pro (flexible) (rigidity)
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2 Coordinate systems: 1) Absolute Cartesian Coordinates
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l02 - 6.581J / 20.482J Foundations of Algorithms and...

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