Data accompanying the PhD dissertation "Structure-Based Prediction of Protein Behavior in Preparative Chromatography"

This repository contains the data generated during the PhD project: Structure-Based Prediction of Protein Behavior in Preparative ChromatographyBy Tim Neijenhuis in Delft University of TechnologySupervisors: Marcel Ottens and Marieke KlijnDepartment of Biotechnology, Section of Bioprocess Engineering.When using the data, please refer using:Neijenhuis, T., Le Bussy, O., Geldhof, G., Klijn, M. E., &amp; Ottens, M. (2024). Predicting protein retention in ion‐exchange chromatography using an open source QSPR workflow. Biotechnology Journal, 19(3), 2300708.Keulen, D., Neijenhuis, T., Lazopoulou, A., Disela, R., Geldhof, G., Le Bussy, O., ... &amp; Ottens, M. (2025). From protein structure to an optimized chromatographic capture step using multiscale modeling. Biotechnology Progress, 41(1), e3505.Disela, R., Neijenhuis, T., Le Bussy, O., Geldhof, G., Klijn, M., Pabst, M., &amp; Ottens, M. (2024). Experimental characterization and prediction of Escherichia coli host cell proteome retention during preparative chromatography. Biotechnology and Bioengineering, 121(12), 3848-3859.<br>The objective of the PhD project was to predict the behavior of proteins for different chromatographic columns using molecular modeling methods.This repository contains all predicted and measured values for each protein for the different columns investigated during the research in a CSV format.These name of each file is identical to the figure presented in the dissertation stating first the chapter followed by the figure (as {chapter}_data_{figure}.csv).

本仓库包含蒂姆·奈延胡斯（Tim Neijenhuis）在代尔夫特理工大学（Delft University of Technology）开展的博士研究项目所生成的实验数据，该项目主题为制备色谱中蛋白质行为的结构预测。本研究的指导教师为马塞尔·奥滕斯（Marcel Ottens）与玛丽克·克林（Marieke Klijn），所属院系为生物技术系生物过程工程研究组。

使用本数据集时，请引用以下文献：
1. 奈延胡斯, T., 勒·比西, O., 格尔德霍夫, G., 克林, M. E., & 奥滕斯, M. (2024). 基于开源定量结构-性质关系（Quantitative Structure-Property Relationship, QSPR）工作流预测离子交换色谱中的蛋白质保留行为. 生物技术期刊, 19(3), 2300708.
2. 克尤伦, D., 奈延胡斯, T., 拉佐普卢, A., 迪塞拉, R., 格尔德霍夫, G., 勒·比西, O., 等, & 奥滕斯, M. (2025). 基于多尺度建模从蛋白质结构实现色谱捕获步骤优化. 生物技术进展, 41(1), e3505.
3. 迪塞拉, R., 奈延胡斯, T., 勒·比西, O., 格尔德霍夫, G., 克林, M., 帕布斯特, M., & 奥滕斯, M. (2024). 制备色谱过程中大肠杆菌宿主细胞蛋白质组保留行为的实验表征与预测. 生物技术与生物工程, 121(12), 3848-3859.

本博士项目的核心目标为，采用分子建模方法预测不同色谱柱条件下的蛋白质行为。本仓库以CSV格式存储了本研究中所有被测蛋白质在各考察色谱柱下的预测值与实测值。每个文件的命名与学位论文中的图表命名规则一致，格式为`{chapter}_data_{figure}.csv`，即先标注章节编号，再跟上对应图表编号。