Skip to main content

Module for analyzing electrostatics with protein structures

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 potential vector fields between 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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

aesop-0.0.8.tar.gz (60.9 kB view details)

Uploaded Source

File details

Details for the file aesop-0.0.8.tar.gz.

File metadata

  • Download URL: aesop-0.0.8.tar.gz
  • Upload date:
  • Size: 60.9 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No

File hashes

Hashes for aesop-0.0.8.tar.gz
Algorithm Hash digest
SHA256 434569b4fd0cd3840088d564cca20e7bef07edf4b914698ea0ba515ba36aa407
MD5 32d96a3a26125e856805b005cbc441d9
BLAKE2b-256 1d51442ff6744eb1ca95e55776c027030e00014266f5d0f431fb21926cdaff81

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page