2014
DOI: 10.1002/prot.24551
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Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction

Abstract: We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality signi… Show more

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Cited by 194 publications
(185 citation statements)
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“…This method has been shown to be effective in describing antibody CDR structures. 26 Thus, modeling of the antibody 001 CDR domains was employed. As seen in Fig.…”
Section: Resultsmentioning
confidence: 99%
“…This method has been shown to be effective in describing antibody CDR structures. 26 Thus, modeling of the antibody 001 CDR domains was employed. As seen in Fig.…”
Section: Resultsmentioning
confidence: 99%
“…The missing region of the AcrA structure was generated by using the SWISS-MODEL homology-modeling server and used to represent the whole structure of AcrA. The AcrA binding site was calculated by using the BioLuminate program in the Schrödinger suite (54). …”
Section: Methodsmentioning
confidence: 99%
“…Although repertoire-wide crystallographic studies are not feasible at present, advances in computational protein modeling have enabled the structure of antibodies having moderate-length CDR loops to be predicted accurately (23)(24)(25)(26). In particular, computational models using RosettaAntibody-predicted X-ray structures within 1-1.5 Å rmsd in framework and canonical loops and 2 Å in CDR-H3 loops (27).…”
Section: Significancementioning
confidence: 99%