CATNAP: a tool to compile, analyze and tally neutralizing antibody panels

CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody. Website name: CATNAP (Compile, Analyze and Tally NAb Panels). Website address: http://hiv.lanl.gov/catnap.

[1]  Thomas B Kepler,et al.  Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors , 2013, F1000Research.

[2]  Ning Ma,et al.  IgBLAST: an immunoglobulin variable domain sequence analysis tool , 2013, Nucleic Acids Res..

[3]  Ron Diskin,et al.  Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design , 2011, Science.

[4]  Pham Phung,et al.  Sequences in Glycoprotein gp41, the CD4 Binding Site, and the V2 Domain Regulate Sensitivity and Resistance of HIV-1 to Broadly Neutralizing Antibodies , 2012, Journal of Virology.

[5]  Patrick Wilson,et al.  iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences , 2007, Bioinform..

[6]  Chaim A. Schramm,et al.  Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus , 2013, Nature.

[7]  Mario Roederer,et al.  Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing , 2011, Science.

[8]  Véronique Giudicelli,et al.  IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. , 2011, Cold Spring Harbor protocols.

[9]  Holly Janes,et al.  Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies , 2009, Journal of Virology.

[10]  Gwo-Yu Chuang,et al.  A Short Segment of the HIV-1 gp120 V1/V2 Region Is a Major Determinant of Resistance to V1/V2 Neutralizing Antibodies , 2012, Journal of Virology.

[11]  Tongqing Zhou,et al.  Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01 , 2010, Science.

[12]  Tongqing Zhou,et al.  Structural definition of a conserved neutralization epitope on HIV-1 gp120 , 2007, Nature.

[13]  Ming Li,et al.  Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies , 2010, PLoS Comput. Biol..

[14]  P. Lipsky,et al.  Characterization of the Human Ig Heavy Chain Antigen Binding Complementarity Determining Region 3 Using a Newly Developed Software Algorithm, JOINSOLVER , 2004, The Journal of Immunology.

[15]  Raphael Gottardo,et al.  Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies , 2013, Journal of Virology.

[16]  D. Montefiori,et al.  Evaluating Neutralizing Antibodies Against HIV, SIV, and SHIV in Luciferase Reporter Gene Assays , 2004, Current protocols in immunology.

[17]  D. Burton,et al.  Highly Antigenically Diverse Viruses Broadly Neutralizing Antibodies Present New Prospects to Counter , 2012 .

[18]  Feng Gao,et al.  Diversity Considerations in HIV-1 Vaccine Selection , 2002, Science.

[19]  Han Gao,et al.  Antibody 8ANC195 reveals a site of broad vulnerability on the HIV-1 envelope spike. , 2014, Cell reports.

[20]  Tongqing Zhou,et al.  PGV04, an HIV-1 gp120 CD4 Binding Site Antibody, Is Broad and Potent in Neutralization but Does Not Induce Conformational Changes Characteristic of CD4 , 2012, Journal of Virology.

[21]  Yan Liu,et al.  A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield , 2011, Science.

[22]  Florian Klein,et al.  Computational analysis of anti–HIV-1 antibody neutralization panel data to identify potential functional epitope residues , 2013, Proceedings of the National Academy of Sciences.

[23]  J. Sodroski,et al.  Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody , 1998, Nature.

[24]  Marie-Paule Lefranc,et al.  IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis , 2008, Nucleic Acids Res..

[25]  Young Do Kwon,et al.  Residue-Level Prediction of HIV-1 Antibody Epitopes Based on Neutralization of Diverse Viral Strains , 2013, Journal of Virology.

[26]  R. Desrosiers,et al.  The Tale of the Long Tail: the Cytoplasmic Domain of HIV-1 gp41 , 2012, Journal of Virology.

[27]  Ron Diskin,et al.  Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding , 2011, Science.

[28]  Adam Godzik,et al.  bNAber: database of broadly neutralizing HIV antibodies , 2013, Nucleic Acids Res..

[29]  Young Do Kwon,et al.  Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9 , 2011, Nature.

[30]  Gwo-Yu Chuang,et al.  NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences , 2014, Nucleic Acids Res..

[31]  James C Paulson,et al.  Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers. , 2014, Immunity.