Residue-wise local quality estimation for protein models from cryo-EM maps.
Residue-wise local quality estimation for protein models from cryo-EM maps.
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DOI：
10.1038/s41592-022-01574-4
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发表时间：
2022-09
期刊：
影响因子：
48
通讯作者：
Kihara, Daisuke
中科院分区：
文献类型：
--
作者：
Terashi, Genki;Wang, Xiao;Subramaniya, Sai Raghavendra Maddhuri Venkata;Tesmer, John J. G.;Kihara, Daisuke
越来越多的蛋白质结构被用低温电子显微镜（cryo-EM）测定。尽管冷冻电镜密度图的分辨率总体上在提高，但仍有许多情况下，蛋白质的氨基酸被分配到不同的置信度水平。在这里，我们开发了一种方法，以识别潜在的错配的残基在地图上，包括残基移位沿着其他正确的主链轨迹。这个分数被称为DAQ，它计算通过深度学习估计的局部密度与不同氨基酸、原子和二级结构对应的可能性，并根据该可能性评估蛋白质结构模型中氨基酸分配的一致性。当DAQ应用于PDB中不同版本的模型结构时，从相同的密度图中得出，在较新版本的模型中观察到DAQ的明显改进。DAQ也发现潜在的错配错误在大量沉积蛋白质结构模型建立在低温电镜图。
An increasing number of protein structures are being determined by cryogenic electron microscopy (cryo-EM). Although the resolution of determined cryo-EM density maps is improving in general, there are still many cases where amino acids of a protein are assigned with different levels of confidence. Here we developed a method that identifies potential misassignment of residues in the map, including residue shifts along an otherwise correct main-chain trace. The score, named DAQ, computes the likelihood that the local density corresponds to different amino acids, atoms, and secondary structures, estimated via deep-learning, and assesses the consistency of the amino acid assignment in the protein structure model with that likelihood. When DAQ was applied to different versions of model structures in PDB that were derived from the same density maps, a clear improvement of DAQ was observed in the newer versions of the models. DAQ also found potential misassignment errors in a substantial number of deposited protein structure models built into cryo-EM maps.
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影响因子：
48
作者：
Barad BA;Echols N;Wang RY;Cheng Y;DiMaio F;Adams PD;Fraser JS
通讯作者：
Fraser JS
DOI：
10.1107/s2059798318009324
发表时间：
2018-09-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
通讯作者：
Urzhumtsev A
DOI：
10.1107/s2059798320014928
发表时间：
2021-01-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Cragnolini T;Sahota H;Joseph AP;Sweeney A;Malhotra S;Vasishtan D;Topf M
通讯作者：
Topf M
影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
DOI：
10.1016/s0097-8485(96)80004-0
发表时间：
1996-03-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Gribskov, M;Robinson, NL
通讯作者：
Robinson, NL