AESOP

AESOP quantifies electrostatic properties of protein families and determines individual amino-acid contributions to electrostatic potentials for comparative analysis.

Key Features:

• Quantitative Electrostatic Comparisons: Performs quantitative analyses of electrostatic potentials across protein family members.
• Amino Acid Contribution Analysis: Computes the contributions of individual amino acids to the overall electrostatic landscape of a protein.
• Parallel Processing Capability: Implemented in Python and supports parallel computations for large-scale analyses.
• Integration with Established Computational Tools: Uses PDB2PQR to assign atomic charges and radii and the Adaptive Poisson-Boltzmann Solver (APBS) to compute grid-based electrostatic potential files.
• Comparison and Perturbation Analysis: Compares sets of electrostatic potentials and generates ensembles of electrostatic potential files for libraries of mutants to quantify effects of structural perturbations.

Scientific Applications:

• Engineering Protein Complexes: Evaluates electrostatic factors that influence protein–protein interactions to inform design of protein complexes.
• Mutagenesis Studies: Models mutant libraries to predict how specific amino acid substitutions alter electrostatic profiles and affect stability or function.
• Drug Design and Development: Analyzes electrostatic interactions to aid rational design of ligands targeting specific proteins and to optimize binding affinity and specificity.

Methodology:

Preparation of protein structures using PDB2PQR to assign atomic charges and radii; computation of grid-based electrostatic potentials with the Adaptive Poisson-Boltzmann Solver (APBS); generation and comparison of electrostatic potential files including ensembles for mutant libraries; implemented in Python with support for parallel processing.