Neutralizing Antibody Resources

Tools

• CATNAP: Compile, Analyze and Tally NAb Panels
  Analysis of panels of antibody data for identification of potential genetic signatures.
  • Database CATNAP analyzes published IC₅₀/IC₈₀ data for anti-HIV neutralizing antibodies.
  • Custom CATNAP analyzes any numerical data associated with a protein alignment.
  • Hybrid CATNAP analyzes your neutralization data together with published data.

• CombiNAber
  Predict the neutralization of combinations of antibodies

• HIV Genome Browser
  A customization of jBrowse displaying genome and proteome features of HIV, including epitopes and neutralizing antibody features.

• External Tools for Germline Antibody Reconstruction
  A list of external computational tools for modeling antibody evolution and germ line reconstruction from antibody or T-cell receptor sequence data.

Search interface

• Neutralizing antibody contexts and features
  Search for locations of important neutralizing antibody binding sites and other HIV-1 Env features.

Tables

• Neutralizing antibody contexts and features (.xls)
  A summary of the information from the search interface above, presented in a single .xls spreadsheet. Each row of the table corresponds to one residue of HIV-1 Env, and each column represents a protein feature or set of known binding residues of broadly neutralizing antibodies. Loops and other features of Env are shown in the first 3 columns on the left. The entropy (sequence variability) of each residue is presented numerically and color coded. Abbreviated references are listed under each column heading, and full references are on the second page of the Excel file.

• Best neutralizing antibodies
  A table presenting the most broadly-neutralizing HIV-1 antibodies, with links to papers, Ab sequences, structures, notes on breadth of neutralization, locations of Ab contacts or key residues, and heavy and light chain composition.

Protocols and Other Data

• Standardized Assessments of Neutralizing Antibodies for HIV/AIDS Vaccine Development Assay protocols from Duke Central Reference Laboratory

• Neutralization Serotype Discovery Panel: A large panel of Env-pseudotyped viruses assayed against plasmas from chronic infection. The panel and plasmas were selected to represent M-group diversity. Access from Special Interest Alignments at the HIV Sequence Database.