Stability determination of Protein Data Bank structures

 

氏名:Gert-Jan Bekker, Mochammad Arfin, Kenji Mizuguchi

所属:Osaka University, Institute for Protein Research

概要:High temperature molecular dynamics (MD) simulations (400 K) can be used as an effective tool to evaluate the stability of proteins (Bekker et al, 2019 doi:10.1002/pro.3546). The Dynamics DataBank (DDB) (https://bsma.pdbj.org/dynamicsdb/) includes the stability analysis of a large number of single-chained Protein Data Bank (PDB) entries. To expand the dataset, we selected several multi-chained PDB entries, and we used the CMC SQUID cluster to perform similar simulations. For 27 multi-chained PDB entries, we performed 10 x 100ns canonical MD simulations at 400 K. After analysis these will be added to the DDB.

 




Posted : 2024年03月31日