lecnotesdec10 - Recent advances in Complexity CIS 6930/CIS...

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Recent advances in Complexity CIS 6930/CIS 4930 December 10, 2002 Lecture Lecture 29 Lecturer: Andrew Lomonosov Scribe: Andrew Lomonosov 1 Molecule A molecule is a group of atoms which remains spatially intact on the time scale of interest. Its structure consists of those features which remain invariant on that time scale. The atoms are bound together by covalent bonds , a very strong link which can be broken only by high temperatures or in chemical reactions. Generally the bond lengths between covalently bonded pairs of atoms have very nearly Fxed values on the order of 1 to 2 angstroms (10 - 10 m). The covalent structure of a molecule is the way in which its atoms are bonded together. The conformation of a molecule is its precise spatial structure at some instant in time. Any conformation can be completely speciFed by giving Cartesian coordinates of all the atoms. It can also be speciFed by giving all interatomic distances. Figure 1 : Example of a covalent structure of a C 8 H 10 N 4 O 2 molecule 2 Molecular modeling Molecular modeling is the science of studying molecular structure and function through model building and computation. It is a multidisciplinary enterprise. It involves biology (cellular picture), chemistry (atomic and molecular details), physics (electronic level and underlying forces), mathe- matics (numerical models and topology) and computer science (algorithms and implementation for large scale problems). Lecture 29-1
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2.1 Brief overview of computational biology Currently term computational biology encompasses virtually all computational approaches to molec- ular biology problems. It can be subdivided into several major parts. One part is bioinformatics that refers to a particular branch of computational biology where the emphasis is on “inference” and datamining/learning from known/mapped patterns (Both nucleic acids and proteins), rather than trying to provide an ab-initio biophysically based model. One particular branch of bioinformatics is chemoinformatics that uses large existing chemical databases for designing new drugs. In bioinformatics approaches we infer the tertiary (3d) structure of a protein from its primary structure by looking at similar primary structures whose tertiary structure is known and doing some sort of learning or extrapolation. We are not interested in giving a biophysical explanation of the primary-tertiary correspondence or map. Contrastingly,in
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lecnotesdec10 - Recent advances in Complexity CIS 6930/CIS...

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