Molecular Dynamics Simulation for Investigating Antigen-Antibody Interaction.
Methods Mol Biol
; 2552: 101-107, 2023.
Article
em En
| MEDLINE
| ID: mdl-36346587
ABSTRACT
Molecular dynamics (MD) simulation is a computational method which elucidates the protein dynamics. Following analyses characterize the dynamics and structural change as well as interaction energy. To characterize the protein structure effectively, the internal angular coordinates are often useful. Directional analysis provides the averages and variances of those coordinates in a mathematically rigorous way. Here, we describe not only a standard MD simulation procedure for the antigen-antibody system but also an umbrella sampling method following a multistep targeted MD simulation (US/mTMD), which is useful for evaluating the free energy profile along the antigen-antibody dissociation coordinate.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Proteínas
/
Simulação de Dinâmica Molecular
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article