Atomic 3D Model of NIST Monoclonal Antibody Reference Material

A 2022 release from the National Institute of Standards and Technology provides an all-atom 3D model of the intact monoclonal antibody Reference Material 8671 (NISTmAb). The dataset includes atomic coordinates in PDB format and the primary sequence in FASTA format to support molecular modeling of whole antibodies.

Use Cases

• Perform molecular dynamics simulations using the atomic coordinates to study hinge region flexibility and antibody function.
• Use the FASTA-formatted primary sequence for homology modeling or sequence alignment with other therapeutic antibodies.
• Validate small-angle scattering data by generating theoretical scattering profiles from the provided PDB-formatted atomic model.
• Analyze the structural configuration of the intact IgG1 mAb, including Fab and Fc domains, for drug design applications.

Strengths

• Model is based on the extensively characterized NIST Reference Material 8671, a standard for antibody research.
• Provides data in multiple standard structural biology formats including PDBv3, FASTA, and MMCIF/PDBX.
• Represents a complete all-atom model of an intact monoclonal antibody, addressing a gap in structural databases focused on fragments.

Limitations

• The model represents a single static or consensus conformation; the dynamic hinge region's flexibility is not captured in the coordinate file.
• No experimental structural data (e.g., X-ray crystallography density maps) are included to validate the modeled coordinates.
• Dataset size and computational resource requirements for simulations are unspecified.

Provenance

Source

National Institute of Standards and Technology

Collection Method

Computational construction of an all-atom 3D model based on the characterized NISTmAb reference material.

Freshness

Last updated in July 2022.