Software
AESOP (Analysis of Electrostatic Structures Of Proteins)
Thank you for your interest to download the AESOP computational framework.
AESOP 0.0.14 is available as a python library at:
https://pypi.python.org/pypi/aesop/
We recommend starting by following the instructions in the aesop.readthedocs.io document.
AESOP has three modules for the analysis of protein electrostatics: (i) alanine scan, (ii) directed mutagenesis, and (iii) electrostatic similarities.
We welcome and encourage collaboration through the AESOP GitHub repository: https://github.com/BioMoDeL/aesop.
An older R version of AESOP is also available by request from biomodel@engr.ucr.edu
AESOP webserver
https://aeolus.engr.ucr.edu/aesop/
The webserver is an efficient option to perform alanine scans of ionizable amino sides, one at a time, and electrostatic analysis of the alanine scan family of structures.
AESOP Developing Team
Biomolecular Modeling & Design Lab (BioMoDeL)
Department of Bioengineering
University of California, Riverside
Web: biomodel.engr.ucr.edu
E-mail: biomodel@engr.ucr.edu
AESOP Developers (2007-)
Reed Harrison, Rohith Mohan, Chris A Kieslich, Ronald D Gorham Jr, Zied Gaieb, Jianfeng Yang, and Dimitrios Morikis.
AESOP Development References
Harrison RES, Mohan RR, Gorham RD Jr, Kieslich CA, Morikis D (2017) AESOP: A Python Library for Investigating Electrostatics in Protein Interactions, Biophysical Journal 112:1761-1766. DOI: http://dx.doi.org/10.1016/j.bpj.2017.04.005.
Gorham RD Jr, Kieslich CA, Morikis D (2011) Electrostatic clustering and free energy calculations provide a foundation for protein design and optimization, Annals of Biomedical Engineering 39:1252-1263.
Kieslich CA, Gorham RD Jr, Morikis D (2011) Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar, Journal of Non-Crystalline Solids 357:707-716.
Kieslich CA, Morikis D, Yang J, Gunopulos D (2011) Automated computational protocol for alanine scans and clustering of electrostatic potentials: application to C3d-CR2 association, Biotechnology Progress 27:316-325.
Gorham RD Jr, Kieslich CA, Nichols A, Sausman NU, Foronda M, Morikis D (2011) An evaluation of Poisson-Boltzmann electrostatic free energy calculations through comparison with experimental mutagenesis data, Biopolymers 95:746-754.
AESOP Applications
López-Perrote A, Harrison RES, Subías M, Alcorlo M, Rodríguez de Córdoba S, Morikis D, Llorca O (2017) Ionic tethering contributes to the conformational stability and function of complement C3b, Molecular Immunology 85:137-147. DOI: http://dx.doi.org/10.1016/j.molimm.2016.12.015.
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.
Harrison R, 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.
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.
Liu Y, Kieslich CA, Morikis D, Liao J (2014) Engineering pre-SUMO4 as efficient substrate of SENP2, Protein Engineering Design & Selection 27: 117-126.
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.
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.
López de Victoria A, Kieslich CA, Rizos AK, Krambovitis E, Morikis D (2012) Clustering of HIV-1 subtypes based on gp120 V3 loop electrostatic properties, BMC Biophysics 5:3.
Gorham RD Jr, 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.
Kieslich CA, Tamamis P, Gorham RD Jr, López de Victoria A, Sausman N, Archontis G, Morikis D (2012) Exploring protein-ligand and protein-protein interactions in the immune system using molecular dynamics and continuum electrostatics, Current Physical Chemistry 2:324-343.
Hakkoymaz H, Kieslich CA, Gorham RD Jr, Gunopulos D, Morikis D (2011) Electrostatic similarity determination using multi-resolution analysis, Molecular Informatics 30:733-746.
El-Assaad AM, Kieslich CA, Gorham RD Jr, 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.
Kieslich C, Vazquez H, Goodman GN, López De Victoria A, Morikis D (2011) The effect of electrostatics on Factor H function and related pathologies, Journal of Molecular Graphics and Modelling 29:1047-1055.
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.
Cheung A, Kieslich C, Yang J, and Morikis D, (2010) Solvation effects in calculated electrostatic association free energies for the C3d-CR2 complex, and comparison to experimental data, Biopolymers 93:509-519.