Primary Citation PubMed: 14981267
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Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
(2007) Genome Biol 8
PubMed: 17335583 | PubMedCentral: PMC1868941 | DOI: 10.1186/gb-2007-8-3-r31
For instance, a typical (κ, α) plot (blue diamond) of an all-β protein (human anti-HIV-1 GP120-reactive antibody E51, PDB code 1RZF-L [ 21 ]) is significantly different from th... t (red cross) of an all-α protein (human hemoglobin, PDB code 1J41-A [ 22 ]).
(a) The typical (κ, α) plots of an all-α protein (Protein Data Bank [PDB] code 1J41-A; red) and an all-β protein (PDB code 1RZF-L; blue).
Publication Year: 2007
Computational docking of antibody-antigen complexes, opportunities and pitfalls illustrated by influenza hemagglutinin.
(2011) Int J Mol Sci 12
PubMed: 21339984 | PubMedCentral: PMC3039950 | DOI: 10.3390/ijms12010226
Rosetta Antibody: 1RZG for the heavy-chain framework (71.68%) and 1RZF for the light chain (64.36%); 1BJM for L1 (same length, no identity), 1RZF for L2 (83.33%), and 1RZF for L3 (90.91%); 1RZG forH1 ... 62.50%), 1RHH for H2 (76.47%), and 1FAI for H3 (same length, no identity).
Publication Year: 2011
Influenza human monoclonal antibody 1F1 interacts with three major antigenic sites and residues mediating human receptor specificity in H1N1 viruses.
(2012) PLoS Pathog 8
PubMed: 23236279 | PubMedCentral: PMC3516549 | DOI: 10.1371/journal.ppat.1003067
Structures from PDB codes 2FB4 and 1RZF (1F1 Fab, variable domains and constant domains, respectively); 1RUZ (Av1918), or the 1F1 Fab and Av1918 coordinates reported here (1F1-SC1918 complex), were us... d as search models and total of 2 Fabs (1F1 Fab), 1 HA trimer (3 protomers) (Av1918), or two HA trimers (six protomers), 2 Fabs, and 4 sets of V H /V λ domains (1F1-SC1918 complex) were ordered in the asymmetric unit.
Publication Year: 2012
Structural basis for the recognition of human cytomegalovirus glycoprotein B by a neutralizing human antibody.
(2014) PLoS Pathog 10
PubMed: 25299639 | PubMedCentral: PMC4192593 | DOI: 10.1371/journal.ppat.1004377
The unrelated Fab fragment of the human anti-HIV-1 gp120 reactive antibody E51 (PDB ID 1rzf) was used as a search model for the SM5-1 Fab structure.
Publication Year: 2014
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