EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Scalable protein design using optimization in a relaxed sequence space.
ジャーナル・号・ページ	Science, Vol. 386, Issue 6720, Page 439-445, Year 2024
掲載日	2024年10月25日
著者	Christopher Frank / Ali Khoshouei / Lara Fuβ / Dominik Schiwietz / Dominik Putz / Lara Weber / Zhixuan Zhao / Motoyuki Hattori / Shihao Feng / Yosta de Stigter / Sergey Ovchinnikov / Hendrik Dietz /
PubMed 要旨	Machine learning (ML)-based design approaches have advanced the field of de novo protein design, with diffusion-based generative methods increasingly dominating protein design pipelines. Here, we ...Machine learning (ML)-based design approaches have advanced the field of de novo protein design, with diffusion-based generative methods increasingly dominating protein design pipelines. Here, we report a "hallucination"-based protein design approach that functions in relaxed sequence space, enabling the efficient design of high-quality protein backbones over multiple scales and with broad scope of application without the need for any form of retraining. We experimentally produced and characterized more than 100 proteins. Three high-resolution crystal structures and two cryo-electron microscopy density maps of designed single-chain proteins comprising up to 1000 amino acids validate the accuracy of the method. Our pipeline can also be used to design synthetic protein-protein interactions, as validated experimentally by a set of protein heterodimers. Relaxed sequence optimization offers attractive performance with respect to designability, scope of applicability for different design problems, and scalability across protein sizes.
リンク	Science / PubMed:39446959 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.1 - 3.36 Å
構造データ	50040 9exk EMDB-50040, PDB-9exk: Scalable protein design using hallucination in a relaxed sequence space 手法: EM (単粒子) / 解像度: 3.36 Å 50113 9f0l EMDB-50113, PDB-9f0l: Scalable protein design using hallucination in a relaxed sequence space 手法: EM (単粒子) / 解像度: 2.76 Å PDB-8s89: Efficient and scalable protein design using a relaxed sequence space 手法: X-RAY DIFFRACTION / 解像度: 2.1 Å PDB-8yl4: Crystal structure of the de novo designed protein 200 AA in the crystal form 1 手法: X-RAY DIFFRACTION / 解像度: 2.88 Å PDB-8yl8: Crystal structure of the de novo designed protein 200 AA in the crystal form 2 手法: X-RAY DIFFRACTION / 解像度: 2.21 Å PDB-9exz: Efficient and scalable protein design using a relaxed sequence space 手法: X-RAY DIFFRACTION / 解像度: 2.8 Å
化合物	ChemComp-SO4: SULFATE ION / 硫酸ジアニオン ChemComp-HOH: WATER ChemComp-GOL: GLYCEROL / グリセロ-ル
由来	synthetic construct (人工物) escherichia coli (大腸菌)
キーワード	DE NOVO PROTEIN / P400 / De novo protein design / De novo designed protein K12 / P600