ARMADiLLO

ARMADiLLO estimates probabilities of amino acid mutations in antibody sequences to analyze somatic hypermutation and support studies of B cell ontogeny and vaccine design, including evaluation of broadly neutralizing antibodies and HIV-related antibody evolution.

Key Features:

• Simulation of Somatic Hypermutation: Simulates somatic hypermutation to model mutation processes that occur during B cell affinity maturation.
• Probability Estimation: Provides probability estimates for all possible amino acid changes across full-length antibody sequences using a DNA sequence context-dependent targeting and substitution model.
• Precomputed Results: Includes precomputed amino acid substitution probabilities for all human V gene segments and a curated collection of HIV broadly neutralizing antibodies.

Scientific Applications:

• B Cell Ontogeny Studies: Analyzes mutation trajectories and probabilities to investigate B cell developmental pathways and affinity maturation.
• Vaccine Design: Identifies developmentally rate-limiting or improbable mutations relevant to strategies for eliciting broadly neutralizing antibodies via vaccination.
• HIV Research: Enables comparative analyses and hypothesis generation using precomputed HIV broadly neutralizing antibody datasets to inform HIV vaccine development.

Methodology:

Uses a DNA sequence context-dependent targeting and substitution model to simulate somatic hypermutation and compute amino acid substitution probabilities.