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Project Description

AESOP

(A)nalysis of (E)lectrostatic (S)tructures (o)f (P)roteins

Authors: Reed Harrison, Rohith Mohan, and Dimitrios Morikis

Framework

  • AESOP is a computational framework to explore electrostatic structures within proteins. The library depends on external tools including: APBS, PDB2PQR, Modeller, and ProDy
  • Atomic Selections
  • Examples
    • All materials for example cases are provided in the tests folder
  • Documentation
    • HTML documentation provided within the docs folder
  • Dependencies
    • APBS and PDB2PQR
    • Required Python libraries: numpy, scipy, prody, matplotlib, modeller, griddataformats
    • Optional Python libraries: multiprocessing

Methods

  • Alascan
    • Perform a computational alanine scan on a provided protein structure using a side-chain truncation scheme
    • Association free energies for mutatants (relative to the parent) may be predicted if 2 or more selection strings are provided
    • Users may restrict mutations to some region of the protein structure
  • DirectedMutagenesis
    • Perform a directed mutagenesis scan on a provided protein structure using Modeller to swap amino acids
    • Association free energies for mutatants (relative to the parent) may be predicted if 2 or more selection strings are provided
    • Mutations must be specified
  • ElecSimilarity
    • Compare electrostatic potentials of multiple protein structures
    • If structures are very dissimilar, the user should superpose coordinates for each protein structure according to their desired method

General Utilities

  • aesop.plotScan()
    • Show bargraph summary of results from computational mutagenesis methods (Alascan, DirectedMutagenesis)
  • aesop.plotESD()
    • Show heatmap summary of results from methods exploring electrostatic similarity (ElecSimilarity)
  • aesop.plotDend()
    • Show dendrogram summary of results from methods exploring electrostatic similarity (ElecSimilarity)

Notes

  • We recommend using Anaconda to aid in installation of Python scientific libraries
  • Depending on your platform, ProDy may need to be installed with an executable
Release History

Release History

1.0.4

This version

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1.0.3

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1.0.2

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1.0.1

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1.0.0

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0.0.17

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0.0.16

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0.0.15

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0.0.14

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0.0.13

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0.0.12

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0.0.11

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0.0.10

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0.0.9

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0.0.8

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0.0.7

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0.0.6

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0.0.5

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0.0.4

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0.0.3

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0.0.2

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0.0.1

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Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
aesop-1.0.4.tar.gz (65.8 kB) Copy SHA256 Checksum SHA256 Source Oct 20, 2016

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