AESOP is a computational framework to investigate electrostatic interactions that promote association
of protein complexes and to compare similarity of electrostatic potentials across families of proteins.
In the former case, protein engineering (or re-engineering) of enzymes or other industrial proteins may
benefit from AESOP by using the software to optimize association of some protein with its binding partner.
In such applications, the activity of the protein system is diffusion-limited. By promoting association,
the protein may be enhanced for its application.
AESOP is developed in the Biomolecular Modeling and design Lab (BioMoDeL) under the supervision of Professor
Dimitrios Morikis. The python library of AESOP is developed by Reed Harrison and Rohith Mohan [Harrison2016], and
is based on the original AESOP framework, written in R, that was developed and parametrized by Chris Kieslich
and Ronald Gorham [Kieslich2011-1] [Gorham2011-1] [Gorham2011-2] [Kieslich2011-2]. A preliminary computational protocol for electrostatic similarities that preceded
AESOP was developed by Jianfeng Yang.
The AESOP acronym stands for Analysis of Electrostatic Structures Of Proteins.
The original AESOP acronym stood for Analysis of Electrostatic Similarities Of Proteins.
|[Harrison2016]||Harrison REH, Mohan RR, Gorham RD Jr, Kieslich CA, Morikis D (2016, in submission) AESOP: A Python Library for Investigating Electrostatics in Protein Interactions|
Published applications of AESOP
The following references are examples of analyses that AESOP can perform.
|[Chen2015]||Chen C, Gorham RD Jr., Gaieb Z, and Morikis D (2015) Electrostatic interactions between complement regulator CD46(SCR1-2) and adenovirus Ad11/Ad21 fiber protein knob, Molecular Biology International, 2015: Article ID 967465. 15 pages. DOI:10.1155/2015/967465.|
|[Harrison2015]||Harrison RES, Gorham RD Jr, Morikis D (2015) Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex, Protein Science 24:789-802. DOI:10.1002/pro.2650.|
|[Mohan2015]||Mohan R, Gorham RD Jr, Morikis D (2015) A theoretical view of the C3d:CR2 binding controversy, Molecular Immunology 64:112:122. DOI:10.1016/j.molimm.2014.11.006.|
|[Liu2014]||Liu Y, Kieslich CA, Morikis D, Liao J (2014) Engineering pre-SUMO4 as efficient substrate of SENP2, Protein Engineering Design & Selection 27:117-126. DOI: 10.1093/protein/gzu004.|
|[Gorham2014]||Gorham RD Jr, Rodriguez W, Morikis D (2014) Molecular analysis of the interaction between staphylococcal virulence factor Sbi-IV and complement C3d, Biophysical Journal 106:1164-1173. DOI: 10.1016/j.bpj.2014.01.033.|
|[Kieslich2012]||Kieslich CA, Morikis D (2012) The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity, PLoS Computational Biology 8:e1002840 (8 pages). DOI: 10.1371/journal.pcbi.1002840.|
|[Bellows-Peterson2012]||Bellows-Peterson ML, Fung H, Floudas CA, Kieslich CA, Zhang L, Morikis D, Wareham KJ, Monk PN, Hawksworth O, Woodruff TM (2012) De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation, Journal of Medicinal Chemistry 55:4159-4168.|
|[Gorham2012]||Gorham Jr RD, Kieslich CA, Morikis D (2012) Complement inhibition by Staphylococcus aureus: electrostatics of C3d-EfbC and C3d-Ehp association, Cellular and Molecular Bioengineering 5:32-43.|
|[El-Assaad2011]||El-Assaad AM, Kieslich CA, Gorham Jr RD, Morikis D (2011) Electrostatic exploration of the C3d-FH4 interaction using a computational alanine scan, Molecular Immunology 48:1844-1850. Erratum (2013) 53:173-174.|
|[Hakkoymaz2011]||Hakkoymaz H, Kieslich CA, Gorham Jr RD, Gunopulos D, Morikis D (2011) Electrostatic similarity determination using multi-resolution analysis, Molecular Informatics 30:733-746.|
|[Kieslich2011-3]||Kieslich CA, Vazquez H, Goodman GN, L?pez de Victoria A, Morikis D (2011) The effect of electrostatics on Factor H function and related pathologies, Journal of Molecular Graphics and Modeling 29:1047-1055.|
|[Chae2010]||Chae K, Gonong BJ, Kim SC, Kieslich CA, Morikis D, Balasubramanian S, Lord EM (2010) A multifaceted study of stigma/style cysteine-rich adhesion (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction, Journal of Experimental Botany 61:4277-4290.|