The ARMADiLLO web server supports most web browsers, including Microsoft Edge, Google Chrome, Apple Safari, and Mozilla Firefox across the major platforms (Windows, MacOS, and Linux). contains precomputed results reporting the probability of amino acid substitutions in all human V gene segments and in a collection of HIV broadly neutralizing antibodies. == Graphical Abstract == == Graphical Abstract. == == INTRODUCTION == B cells develop receptors that can specifically recognize pathogens through an evolutionary process called affinity maturation which involves iterative rounds of somatic hypermutation (SHM) and antigenic selection within germinal centers (1). After B cells attain specificity to antigen, they can differentiate into plasma cells which secrete the soluble form of the B cell receptor as antibodies or into memory B cells which form the basis of immunological memory and guard against subsequent re-infection with the same or comparable pathogen (2). Advances in antibody cloning and high throughput sequencing methods have resulted in a ARQ 197 (Tivantinib) wealth of antibody sequencing data which has led to a greater understanding of B cell clonal evolution (35). Antibody sequences can be grouped into clones based on shared immunogenetics and these clonally related sequences can then be used as input to phylogenetic methods for inferring an unmutated common ancestor (UCA) sequence that represents the B cell receptor of the original B cell progenitor of the clone prior to affinity maturation (6). Mutations are then identified as differences between an observed antibody sequence and its UCA. The mutational agent that mediates somatic hypermutation in the germinal center, the anatomical microenvironment within lymphoid tissues in which affinity maturation takes place, is usually activation-induced cytidine deaminase (AID) (7). AID preferentially targets specific sequence motifs for mutation (AID hot spots) and demonstrates bias against mutating other sequence motifs (AID cold spots) (8). Due to the sequence context-dependence of AID activity, certain mutations are much more likely to occur than others (9). Amino acid changes that require multiple base substitutions to co-occur within a codon to attain a specific amino acid are also of low probability. We previously developed a computational program, Antigen Receptor Mutation Analyzer for Detection of Low Likelihood Occurrences (ARMADiLLO) to perform simulations of the somatic hypermutation process and draw upon these simulations to estimate the probabilities of amino acid substitutions in the absence of antigenic selection (9). Using ARMADiLLO, we showed that improbable mutations occur with high frequency in HIV broadly neutralizing antibodies (bnAbs) and that improbable mutations are often functionally required for these antibodies to neutralize diverse strains of HIV (9). Critical improbable mutations can act as rate-limiting actions in the development ARQ 197 (Tivantinib) of bnAbs, and thus are high-value targets for selection by immunogens employed in vaccine strategies that aim to recapitulate the induction of comparable types of antibodies in vaccinees using modern vaccine development approaches (1012). Additionally, estimates of mutation probability can help the Rabbit Polyclonal to CDK8 immunologist or vaccinologist determine whether recurrent patterns of mutations arose simply by chance in the absence of selection due to AID activity or were due to selection by the vaccine (13). To make antibody mutation ARQ 197 (Tivantinib) probability analysis accessible to a wider user base, we have developed the ARMADiLLO web server (https//armadillo.dhvi.duke.edu). This web server provides a user-friendly interface for running ARMADiLLO geared towards immunologists and vaccinologists. The ARMADiLLO web server includes several features not previously available in the command-line version of ARMADiLLO including automatic inference of a UCA for the input antibody sequence using the Cloanalyst immunogenetics analysis software (14) while also providing an alternative manual input option for the user to enter a previously inferred UCA. Additionally, the web server allows ARQ 197 (Tivantinib) users to download high-resolution images of the generated results. Finally, the ARMADiLLO web server contains precomputed results reporting the probability of amino acid substitution in all human V gene segments as well as precomputed results for a representative set of 32 HIV bnAbs. Thus, the ARMADiLLO web server is an easy-to-use tool and resource for researchers to perform antibody.