Back to Search
Start Over
<scp>RosettaCM</scp> for antibodies with very long <scp>HCDR3s</scp> and low template availability
- Source :
- Proteins
- Publication Year :
- 2021
- Publisher :
- Wiley, 2021.
-
Abstract
- Antibody-antigen co-crystal structures are a valuable resource for the fundamental understanding of antibody-mediated immunity. Determination of structures with antibodies in complex with their antigens, however, is a laborious task without guarantee of success. Therefore, homology modeling of antibodies and docking to their respective-antigens has become a very important technique to drive antibody and vaccine design. The quality of the antibody modeling process is critical for the success of these endeavors. Here, we compare different computational protocols for predicting antibody structure from sequence in the biomolecular modeling software Rosetta - all of which use multiple existing antibody structures to guide modeling. Specifically, we compare protocols developed solely to predict antibody structure (RosettaAntibody, AbPredict) with a universal homology modeling protocol (RosettaCM). Following recent advances in homology modeling with multiple templates simultaneously, we propose that the use of multiple templates over the same antibody regions may improve modeling performance. To evaluate whether multi-template comparative modeling with RosettaCM can improve the modeling accuracy of antibodies over existing methods, this study compares the performance of the three modeling algorithms when modeling human antibodies taken from antibody-antigen co-crystal structures. In these benchmarking experiments, RosettaCM outperformed other methods when modeling antibodies with long HCDR3s and few available templates.
- Subjects :
- Modeling software
Protein Conformation
Computer science
Process (engineering)
Antigen-Antibody Complex
Computational biology
Molecular Dynamics Simulation
Biochemistry
Antibodies
Article
Structural Biology
Humans
Homology modeling
Antigens
Databases, Protein
Molecular Biology
Protocol (science)
biology
Molecular Docking Simulation
Benchmarking
Template
Structural Homology, Protein
Docking (molecular)
Benchmark (computing)
biology.protein
Antibody
Algorithms
Software
Subjects
Details
- ISSN :
- 10970134 and 08873585
- Volume :
- 89
- Database :
- OpenAIRE
- Journal :
- Proteins: Structure, Function, and Bioinformatics
- Accession number :
- edsair.doi.dedup.....439abb6d8ab5238e1e9a88274891e031