AESOP: A Python Library for Investigating Electrostatics in Protein Interactions

Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion...

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Veröffentlicht in:Biophysical journal 2017-05, Vol.112 (9), p.1761-1766
Hauptverfasser: Harrison, Reed E.S., Mohan, Rohith R., Gorham, Ronald D., Kieslich, Chris A., Morikis, Dimitrios
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container_end_page 1766
container_issue 9
container_start_page 1761
container_title Biophysical journal
container_volume 112
creator Harrison, Reed E.S.
Mohan, Rohith R.
Gorham, Ronald D.
Kieslich, Chris A.
Morikis, Dimitrios
description Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association.
doi_str_mv 10.1016/j.bpj.2017.04.005
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subjects Alanine - chemistry
Alanine - metabolism
Algorithms
Amino acids
Computation
Computational Tools
Computer applications
Diffusion
Diffusion rate
Electric fields
Electrostatic properties
Electrostatics
Enzymes
Internet
Mutants
Mutation
Protein families
Protein interaction
Protein structure
Proteins
Proteins - chemistry
Proteins - genetics
Proteins - metabolism
Python
Software
Static Electricity
Thermodynamics
title AESOP: A Python Library for Investigating Electrostatics in Protein Interactions
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