SAPPHIRE/SUITE: Structural-energetic Analysis Program for Predicting Humoral Immune Response Epitopes/SAPPHIRE User Interface Tool Ensemble

Links to web interfaces for components of SAPPHIRE/SUITE:

1. PACT: represents disordered regions in PDB-style format (e.g., for use with INCA)
2. INCA: uses naccess to generate naccess-style ASA data from PDB-style data
3. SPIRE: zeroes ASA for residues inaccessible to large probe sphere using molmol
4. RACE: zeroes ASA for atoms within spherical or cylindrical regions
5. LACE: zeroes ASA for residues/atoms on user-specified list
6. SUIT: uses SAPPHIRE to estimate binding affinity for candidate B-cell epitopes

Notes:

1. SAPPHIRE/SUITE estimates paratope-binding affinity for candidate B-cell epitopes of peptidic antigens (e.g., for antipeptide antibodies reacting with peptides or cross-reacting with proteins).
2. SAPPHIRE accepts naccess-style ASA data (via SUIT, which reports SAPPHIRE-estimated binding affinity as dissociation-constant values), although naccess is external to SAPPHIRE/SUITE.
3. PDB data may be used directly as input (e.g., for naccess via INCA) if these represent a peptidic-antigen structure having complete atomic coordinates for only non-H atoms.
4. H atoms (e.g., in NMR structure) may be removed and missing (e.g., sidechain) non-H atoms reconstructed (e.g., using spdbv) to yield structure data suitable as input (e.g., for PACT).
5. Disordered residues (which lack well-defined atomic coordinates) may be represented (with or without ordered residues, which have well-defined atomic coordinates) using PACT.

References:

1. Caoili SE (2006) A structural-energetic basis for B-cell epitope prediction. Protein & Peptide Letters 13(7):743-751 (PMID: 17018020)
2. Caoili SE (2010) Immunization with peptide-protein conjugates: impact on benchmarking B-cell epitope prediction for vaccine design. Protein & Peptide Letters 17(3):386-398 (PMID: 19594433)
3. Caoili SE (2012) On the meaning of affinity limits in B-cell epitope prediction for antipeptide antibody-mediated immunity. Advances in Bioinformatics 2012:346765, doi: 10.1155/2012/346765 (PMID: 23209458)
4. Caoili SE (2014) Benchmarking B-cell epitope prediction with quantitative dose-response data on antipeptide antibodies: towards novel pharmaceutical product development. BioMed Research International 2014:867905, doi: 10.1155/2014/867905 (PMID: 24949474)
5. Caoili SE (2014) Hybrid methods for B-cell epitope prediction. Methods in Molecular Biology 1184:245-283, doi: 10.1007/978-1-4939-1115-8_14 (PMID: 25048129)
6. Caoili SE (2015) An integrative structure-based framework for predicting biological effects mediated by antipeptide antibodies. Journal of Immunological Methods 427:19-29, doi: 10.1016/j.jim.2015.09.002 (PMID: 26410103)

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