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• W2071200955 abstract "Abstract High‐resolution homology models are useful in structure‐based protein engineering applications, especially when a crystallographic structure is unavailable. Here, we report the development and implementation of RosettaAntibody, a protocol for homology modeling of antibody variable regions. The protocol combines comparative modeling of canonical complementarity determining region (CDR) loop conformations and de novo loop modeling of CDR H3 conformation with simultaneous optimization of V L ‐V H rigid‐body orientation and CDR backbone and side‐chain conformations. The protocol was tested on a benchmark of 54 antibody crystal structures. The median root mean square deviation (rmsd) of the antigen binding pocket comprised of all the CDR residues was 1.5 Å with 80% of the targets having an rmsd lower than 2.0 Å. The median backbone heavy atom global rmsd of the CDR H3 loop prediction was 1.6, 1.9, 2.4, 3.1, and 6.0 Å for very short (4–6 residues), short (7–9), medium (10–11), long (12–14) and very long (17–22) loops, respectively. When the set of ten top‐scoring antibody homology models are used in local ensemble docking to antigen, a moderate‐to‐high accuracy docking prediction was achieved in seven of fifteen targets. This success in computational docking with high‐resolution homology models is encouraging, but challenges still remain in modeling antibody structures for sequences with long H3 loops. This first large‐scale antibody–antigen docking study using homology models reveals the level of “functional accuracy” of these structural models toward protein engineering applications. Proteins 2009; 74:497–514. © 2008 Wiley‐Liss, Inc." @default.
• W2071200955 created "2016-06-24" @default.
• W2071200955 creator A5009383312 @default.
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• W2071200955 date "2008-11-17" @default.
• W2071200955 modified "2023-10-18" @default.
• W2071200955 title "Toward high-resolution homology modeling of antibody F_vregions and application to antibody-antigen docking" @default.
• W2071200955 cites W1499835878 @default.
• W2071200955 cites W1548178570 @default.
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• W2071200955 cites W1583192328 @default.
• W2071200955 cites W1965530007 @default.
• W2071200955 cites W1966140823 @default.
• W2071200955 cites W1968178110 @default.
• W2071200955 cites W1968922152 @default.
• W2071200955 cites W1969407832 @default.
• W2071200955 cites W1981494014 @default.
• W2071200955 cites W1982679430 @default.
• W2071200955 cites W1987660955 @default.
• W2071200955 cites W1989320890 @default.
• W2071200955 cites W1993955625 @default.
• W2071200955 cites W2000443388 @default.
• W2071200955 cites W2005825070 @default.
• W2071200955 cites W2015392953 @default.
• W2071200955 cites W2018410079 @default.
• W2071200955 cites W2023505225 @default.
• W2071200955 cites W2030074569 @default.
• W2071200955 cites W2043488172 @default.
• W2071200955 cites W2051030846 @default.
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• W2071200955 cites W2075770210 @default.
• W2071200955 cites W2076753628 @default.
• W2071200955 cites W2080500765 @default.
• W2071200955 cites W2083028331 @default.
• W2071200955 cites W2083997681 @default.
• W2071200955 cites W2094967734 @default.
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• W2071200955 cites W2123028643 @default.
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• W2071200955 cites W2167795220 @default.
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• W2071200955 doi "https://doi.org/10.1002/prot.22309" @default.
• W2071200955 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2909601" @default.
• W2071200955 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19062174" @default.
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