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
All selection strings must be made according to the style of ProDy (http://prody.csb.pitt.edu/manual/reference/atomic/select.html)
- 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
1 maintainer
Release files for aesop 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| aesop-1.1.0.tar.gz | 71.5 kB | Details |
Release files / aesop-1.1.0.tar.gz
| Download URL | aesop-1.1.0.tar.gz |
|---|---|
| Size | 71.5 kB |
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