Automated antibody structure prediction using Accelrys tools: results and best practices.

ABSTRACT: We describe the methodology and results from our participation in the second Antibody Modeling Assessment experiment. During the experiment we predicted the structure of eleven unpublished antibody Fv fragments. Our prediction methods centered on template-based modeling; potential templates were selected from an antibody database based on their sequence similarity to the target in the framework regions. Depending on the quality of the templates, we constructed models of the antibody framework regions either using a single, chimeric or multiple template approach. The hypervariable loop regions in the initial models were rebuilt by grafting the corresponding regions from suitable templates onto the model. For the H3 loop region, we further refined models using ab initio methods. The final mo

SUBMITTER: Fasnacht M 

PROVIDER: S-EPMC4312887 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature