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 significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived anti

SUBMITTER: Zhu K 

PROVIDER: S-EPMC5282925 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature