Second antibody modeling assessment (AMA-II)
Abstract
To assess the state of the art in antibody 3D modeling, 11 unpublished high-resolution x-ray Fab crystal structures from diverse species and covering a wide range of antigen-binding site conformations were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. The participants included: Accerlys Inc, Chemical Computer Group (CCG), Schrodinger, Jeff Gray's lab at John Hopkins University, Macromoltek, Astellas Pharma/Osaka University and Prediction of ImmunoGlobulin Structure (PIGS). The sequences of benchmark structures were submitted to the modelers and PIGS, and a set of models were generated for each structure. We provide here an overview of the organization, participants and main results of this second antibody modeling assessment (AMA-II). Also, we compare the results with the first antibody assessment published in this journal (Almagro et al., 2011;79:3050).
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The high degree of antibody sequence and structure conservation in the framework region and the five canonical loops leads to an overall high accuracy of antibody homology modelling.
“The high degree of antibody sequence and structure conservation in the framework region and the five canonical loops leads to an overall high accuracy of antibody homology modelling [7].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [7]
AMA II reported that the overall accuracy of modelling the entire antibody FV is 1.1 Å RMSD on average.
“AMA II reported that the overall accuracy of modelling the entire antibody FV is 1.1 Å Root Mean Square Deviation (RMSD) on average, with the most challenging region being the CDRH3, which is modelled to >5 Å RMSD in some targets.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [7]
CDRH3 is the most challenging region and is modelled to >5 Å RMSD in some targets.
“AMA II reported that the overall accuracy of modelling the entire antibody FV is 1.1 Å Root Mean Square Deviation (RMSD) on average, with the most challenging region being the CDRH3, which is modelled to >5 Å RMSD in some targets.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [7]
Despite different run times, antibody modelling tools produce comparable results.
“Despite different run times, the tools produce comparable results as exemplified by the Antibody Modelling Assessment II [7], a benchmarking experiment in which blinded predictions using some of the aforementioned tools were conducted.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [7]
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- Authors
- Almagro, J. C., Teplyakov, A., Luo, J., Sweet, R. W., Kodangattil, S., Hernandez‐Guzman, F., & Gilliland, G. L.
- Affiliations
- Pfizer (United States) (US)
- Biotechnology Center of Excellence Janssen R&D, LLC. 1400 McKean Road Spring House PA 19477
- Accelrys, Inc. San Diego CA
- Corresponding author
- Almagro, Juan C.
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- Wiley
- Published
- 2014-04-26
- Volume
- 82
- Issue
- 8
- Pages
- 1553-1562
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W1891993075
- Cited by
- 144
- References
- 21
- Citations by year
- 2026: 8 · 2025: 2 · 2024: 9 · 2023: 17 · 2022: 13 · 2021: 8 · 2020: 8 · 2019: 18 · 2018: 16 · 2017: 15 · 2016: 14 · 2015: 8 · 2014: 8
- FWCI
- 6.15
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- Fab crystal structure, pigs
- MeSH terms
- Amino Acid Sequence, Animals, Binding Sites, Antibody, Humans, Immunoglobulin Fab Fragments, Models, Molecular, Molecular Sequence Data, Protein Conformation, Rabbits, Crystallography, X-Ray, Mice
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