AlphaFold and Boltz-2 structural models of NRC2 coiled-coil oligomers and INF1–lipid complexes (Figure 4 of Kourelis, Bentham & Bozkurt, 2026

This deposit contains the predicted structural models used to generate Figure 4 of Kourelis, Bentham & Bozkurt, Computational biology for plant immunity: from structure prediction and protein–protein interactions to bioengineered disease resistance (submitted to New Phytologist). The review synthesises recent advances in AI-driven structure prediction, protein–protein interaction modelling, and computational protein design for plant immunity. The models archived here illustrate specific examples discussed in Figure 4 and are released to enable inspection, verification and reuse. Contents fold_nrc2_cc_domain_only_6x/ — AlphaFold 3 model of the Nicotiana benthamiana NRC2 coiled-coil (CC) domain as a hexamer (apo form). fold_nrc2_cc_domain_only_6x_20xole/ — AlphaFold 3 model of the N. benthamiana NRC2 CC-domain hexamer with 20 molecules of oleic acid bound. INF1-BetaSitesterol/ — Boltz-2 model of the Phytophthora infestans elicitin INF1 in complex with β-sitosterol. INF1-OleicAcid/ — Boltz-2 model of P. infestans INF1 in complex with oleic acid. Each folder contains the predicted structure file(s) (CIF/PDB), the input protein sequence(s) in FASTA, the ligand SMILES where applicable, the run configuration, and per-model confidence outputs (pLDDT, PAE and where applicable ipTM/pTM for AlphaFold; pLDDT, PAE, ipTM, ligand ipTM, PTM and affinity scores for Boltz-2). Methods The Nicotiana benthamiana NRC2 CC-domain hexamer models (apo and with 20 molecules of oleic acid) were generated with AlphaFold 3 via the AlphaFold Server (https://alphafoldserver.com/). The Phytophthora infestans INF1 ligand complexes were generated with Boltz-2 via the Neurosnap web interface (https://neurosnap.ai/), with ligands supplied as SMILES: Oleic acid: CCCCCCCC/C=C\CCCCCCCC(=O)O β-Sitosterol: CC[C@H](CC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C)C(C)C Input protein sequences were obtained from UniProt ([NRC2 accession]; INF1: P15570). Default settings were used throughout; predictions were run between [month year] and [month year], and the exact inputs and outputs for each run are preserved in the corresponding folder. Reuse and citation These models are released under the Creative Commons Attribution 4.0 International (CC-BY 4.0) licence. If you use them, please cite this Zenodo deposit together with the associated New Phytologist review (citation and DOI will be added here once published; the paper's DOI will also be linked via the "Is supplement to" related identifier).本数据集包含用于生成Kourelis、Bentham与Bozkurt投稿至《新植物学家》（New Phytologist）的综述《植物免疫计算生物学：从结构预测、蛋白质-蛋白质相互作用到生物工程抗病性》中图4的预测结构模型。 该综述总结了AI驱动的结构预测、蛋白质-蛋白质相互作用建模以及植物免疫领域计算蛋白质设计的最新进展。此处归档的模型展示了文中图4所讨论的具体实例，公开发布以供检视、验证与复用。 ## 数据集内容 fold_nrc2_cc_domain_only_6x/ —— 本氏烟草（Nicotiana benthamiana）NRC2卷曲螺旋（coiled-coil，CC）结构域六聚体的AlphaFold 3模型（无配体态，apo form）。 fold_nrc2_cc_domain_only_6x_20xole/ —— 结合20分子油酸的本氏烟草NRC2 CC结构域六聚体的AlphaFold 3模型。 INF1-BetaSitesterol/ —— 与β-谷甾醇结合的致病疫霉（Phytophthora infestans）激发素INF1的Boltz-2模型。 INF1-OleicAcid/ —— 与油酸结合的致病疫霉INF1的Boltz-2模型。 每个文件夹均包含预测结构文件（CIF/PDB格式）、FASTA格式的输入蛋白质序列、适用时的配体SMILES字符串、运行配置文件，以及各模型的置信度输出结果（AlphaFold 3模型对应pLDDT、PAE及适用时的ipTM/pTM；Boltz-2模型对应pLDDT、PAE、ipTM、配体ipTM、PTM及亲和力评分）。 ## 实验方法 本氏烟草NRC2 CC结构域六聚体模型（无配体态与结合20分子油酸态）通过AlphaFold服务器（https://alphafoldserver.com/）使用AlphaFold 3生成。致病疫霉INF1配体复合物通过Neurosnap网页界面（https://neurosnap.ai/）使用Boltz-2生成，配体以SMILES格式提供： 油酸：CCCCCCCC/C=CCCCCCCCC(=O)O β-谷甾醇：CC[C@H](CC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C)C(C)C 输入蛋白质序列获取自UniProt（Universal Protein Resource）数据库（[NRC2登录号]；INF1登录号：P15570）。全程使用默认参数；预测运行于[月份 年份]至[月份 年份]之间，各次运行的精确输入与输出均保留在对应文件夹中。 ## 重用与引用 本数据集采用知识共享署名4.0国际许可协议（CC-BY 4.0）发布。若使用本数据集，请同时引用本Zenodo数据集及相关的《新植物学家》综述文章（引用信息与DOI将在论文正式发表后补充至此；论文DOI也将通过"Is supplement to"相关标识符链接）。