Python Programming for Biology: Bioinformatics and Beyond

2

HIV, which causes AIDS, is an example.

3

Strictly speaking a population rather than an individual.

4

Drosphila melanogaster.

5

 Saitou,  N.,  and  Nei,  M.  (1987).  The  neighbor-joining  method:  a  new  method  for

reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4): 406–425.

6

Felsenstein, J. (1989). PHYLIP – Phylogeny Inference Package (Version 3.2). Cladistics

5: 164–166.

7

Here we are using a list of lists, but we could use NumPy arrays.

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Macromolecular structures

Contents

An introduction to 3D structures of bio-molecules

Protein structure

Membrane proteins

RNA structure

Determining macromolecular structures

Using Python for macromolecular structures

Obtaining structure data

Simple geometric manipulations

Representing structures as NumPy arrays

Distances and angles

Structural subsets

Coordinate superimposition

Centring coordinates

Aligning coordinates

Calculating root-mean-square deviation

Aligning a structure ensemble

Homologous structure alignment

External macromolecular structure modules

Structures in BioPython

Structures in PyMol