Spatial and Sequential Topological Analysis of Molecular Dynamics Simulations of IgG1 Fc Domains.

IF 5.7 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2025-04-22 DOI:10.1021/acs.jctc.5c00161

Melinda Kleczynski,Christina Bergonzo,Anthony J Kearsley

引用次数: 0

Abstract

Monoclonal antibodies are utilized in a wide range of biomedical applications. The NIST monoclonal antibody is a resource for developing analysis methods for monoclonal antibody based biopharmaceutical platforms. Techniques from topological data analysis quantify structural features such as loops and tunnels which are not easily measured by classical data analysis methods. In this paper, we introduce the Gaussian CROCKER column differences (GCCD) matrix, which augments standard topological data analysis summaries with biological sequence information. We use GCCD matrices to successfully differentiate between glycosylated and aglycosylated conformations from molecular dynamics simulations of the NIST monoclonal antibody Fc domain. We are optimistic that other researchers will be able to utilize GCCD matrices to quantify multiscale spatial and sequential features.

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IgG1 Fc结构域分子动力学模拟的空间和顺序拓扑分析。

单克隆抗体广泛应用于生物医学领域。NIST 单克隆抗体是为基于单克隆抗体的生物制药平台开发分析方法的资源。拓扑数据分析技术可量化结构特征，如经典数据分析方法不易测量的环路和隧道。本文介绍了高斯 CROCKER 列差（GCCD）矩阵，它利用生物序列信息增强了标准拓扑数据分析总结。我们利用 GCCD 矩阵成功地区分了 NIST 单克隆抗体 Fc 结构域分子动力学模拟中的糖基化构象和糖基化构象。我们相信，其他研究人员也能利用 GCCD 矩阵量化多尺度空间和序列特征。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.