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PDBsum entry 4m7k
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Immune system
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PDB id
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4m7k
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References listed in PDB file
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Key reference
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Title
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Antibody modeling assessment ii. Structures and models.
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Authors
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A.Teplyakov,
J.Luo,
G.Obmolova,
T.J.Malia,
R.Sweet,
R.L.Stanfield,
S.Kodangattil,
J.C.Almagro,
G.L.Gilliland.
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Ref.
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Proteins, 2014,
82,
1563-1582.
[DOI no: ]
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PubMed id
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Abstract
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To assess the state-of-the-art in antibody structure modeling, a blinded study
was conducted. Eleven unpublished Fab crystal structures were used as a
benchmark to compare Fv models generated by seven structure prediction
methodologies. In the first round, each participant submitted three non-ranked
complete Fv models for each target. In the second round, CDR-H3 modeling was
performed in the context of the correct environment provided by the crystal
structures with CDR-H3 removed. In this report we describe the reference
structures and present our assessment of the models. Some of the essential
sources of errors in the predictions were traced to the selection of the
structure template, both in terms of the CDR canonical structures and VL/VH
packing. On top of this, the errors present in the Protein Data Bank structures
were sometimes propagated in the current models, which emphasized the need for
the curated structural database devoid of errors. Modeling non-canonical
structures, including CDR-H3, remains the biggest challenge for antibody
structure prediction. Proteins 2014; 82:1563-1582. © 2014 Wiley Periodicals,
Inc.
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