Primary Citation PubMed: 9380672
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Antibody-protein interactions: benchmark datasets and prediction tools evaluation.
(2007) BMC Struct Biol 7
PubMed: 17910770 | PubMedCentral: PMC2174481 | DOI: 10.1186/1472-6807-7-64
Two epitopes, cetuximab on EGFR [PDB:1YY9] and 7E2C50S on cytochrome c oxidase [PDB:1AR1], appeared to be difficult to predict; they could probably be predicted using the ConSurf average score in comb... nation with a patch generation method.
Similarly, recognition of epitopes on subunit II of cytochrome c oxidase [PDB:1AR1] appears problematic because the protein possesses long protruded α-helixes.
Publication Year: 2007
Prediction of antigenic epitopes on protein surfaces by consensus scoring.
(2009) BMC Bioinformatics 10
PubMed: 19772615 | PubMedCentral: PMC2761409 | DOI: 10.1186/1471-2105-10-302
Methods Protein datasets Protein Dataset 1 48 antigen-antibody complexes with resolution <3.0 Å were selected from the 59 representative antigen-antibody complexes compiled by Ponomare... ko and Bourne[ 25 ]: 2ADF , 1FE8 , 1BGX , 1E6J , 1EGJ , 1FSK , 1H0D , 1IQD , 1JRH , 1LK3 , 1MHP , 1NL0 , 1NSN , 1OAZ , 1ORS , 1PKQ , 1RJL , 1SY6 , 1TZI , 1WEJ , 1YJD , 1YY9 , 1ZTX , 2JEL , 1A14 , 1NCA , 1BVK , 1JHL , 1NDG , 1P2C , 1JPS , 1AR1 , 1EO8 , 1QFU , 1EZV , 1OSP , 1FJ1 , 1FNS , 1G9M , 1R3J , 1N8Z , 1NFD , 1TQB , 2VDL , 1V7M , 1XIW , 2AEP , and 1R0A .
Publication Year: 2009
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins.
(2010) BMC Bioinformatics 11
PubMed: 20420672 | PubMedCentral: PMC2876129 | DOI: 10.1186/1471-2105-11-204
The structural motif associated to the sequence pattern contains the highly conserved residues Tyr167, Pro168, Pro169 and Leu179 (PDB ID: 1ar1 , chain: A) which seem to form a highly structured cytopl... smic loop with the function of placing Trp164 at the right distance from and orientation with respect to heme a 3 .
PDB ID: 1ar1 , chain A, cytochrome c oxidase.
The pattern we find is not documented in any protein motif databases, but it is worthwhile to investigate its function as it contains a tryptophane residue (Trp164, PDB ID: 1ar1 , chain A) which has been widely documented in literature.
Publication Year: 2010
Stacking and energetic contribution of aromatic islands at the binding interface of antibody proteins.
(2010) Immunome Res 6 Suppl 1
PubMed: 20875152 | PubMedCentral: PMC2946779 | DOI: 10.1186/1745-7580-6-S1-S1
(A) Aromatic Island size of 4 at the binding interface of antibody 9D7 and IL-10 (PDB code 1lk3) (B) Aromatic Island size of 5 at the binding interface of antibody 33H1 and potassium channel molecule ... PDB code 1ors) (C) Aromatic Island size of 6 at the binding interface of antibody and cytochrome AA3 (PDB code 1ar1) (D) Aromatic Island size of 7 at the binding interface of antibody YTS 105.18 and T-cell surface glycoprotein CD8 alpha chain (PDB code 2arj) (E) Aromatic Island size of 8 at the binding interface of antibody HyHEL-26 and HEL (PDB code 1ndm) (F) Aromatic Island size of 9 at the binding interface of antibody HyHEL-10 mutant and HEL (PDB code 2eiz) Energetic contribution of “Aromatic Island” to binding affinity It is well known that the abundant stacking of aromatic rings can produce strong and extra effects to stabilize the structures for nucleic acids [ 31 , 32 ].
B-cell epitope prediction through a graph model.
(2012) BMC Bioinformatics 13 Suppl 17
PubMed: 23281855 | PubMedCentral: PMC3521413 | DOI: 10.1186/1471-2105-13-S17-S20
Interacting with an antibody (PDB complex 1AR1).
Taking PDB entry 1AR1 as example again (Figure 1 ), its epitope consists of 19 residues, and the non-planarity of this epitope is as small as 1.08Å, indicating a very flat surface area.
Publication Year: 2012
Reliable B cell epitope predictions: impacts of method development and improved benchmarking.
(2012) PLoS Comput Biol 8
PubMed: 23300419 | PubMedCentral: PMC3531324 | DOI: 10.1371/journal.pcbi.1002829
The PDB files were further processed into 2 different files: 1) only containing the chain interacting with the antibody as original defined in the DiscoTope dataset and 2) PDB files containing additio... al structural information on the biological relevant unit (as described in the publication associated with the structure) if available (obtainable for PDB entry: 1XIW, 1TZH, 1CZ8, 1BJ1, 1K4D, 1K4C, 1KYO, 1EZV, 1NCA, 1NMC, 1A14, 1NCB, 1NCC, 1NCD, 1OTS, 1AR1, 1NFD, 2HMI, 1EO8, 1QFU).
PubMed ID is not available.
Published in 2015
For example, the epitope site Val206 of paracoccus denitrificans two-subunit cytochrome C oxidase complex (PDB ID:1AR1:B) has an RSA value of 0.008.
Publication Year: 2015
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