Prediction of protein stability changes upon single-point variant using 3D structure profile.
Prediction of protein stability changes upon single-point variant using 3D structure profile.
复制标题
使用3D结构曲线对蛋白质稳定性的预测在单点变体上变化。
DOI：
10.1016/j.csbj.2022.12.008
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发表时间：
2023
影响因子：
6
通讯作者：
Xu, Dong
中科院分区：
文献类型：
--
作者：
Gong, Jianting;Wang, Juexin;Zong, Xizeng;Ma, Zhiqiang;Xu, Dong
Overview of feature extraction and feature processing for MU3DSP. MU3DSP starts from sequence to predict , which can achieve real-time prediction. MU3DSP fuses information from 3D structure profiles and sequence. The tertiary structure for MU3DSP does not have to be available. MU3DSP extract multiple descriptors from wild-type and mutated protein structures. Mutation-based structures are from either homology models or G2S database. Identifying protein thermodynamic stability changes upon single-point variants is crucial for studying mutation-induced alterations in protein biophysics, genomic variants, and mutation-related diseases. In the last decade, various computational methods have been developed to predict the effects of single-point variants, but the prediction accuracy is still far from satisfactory for practical applications. Herein, we review approaches and tools for predicting stability changes upon the single-point variant. Most of these methods require tertiary protein structure as input to achieve reliable predictions. However, the availability of protein structures limits the immediate application of these tools. To improve the performance of a computational prediction from a protein sequence without experimental structural information, we introduce a new computational framework: MU3DSP. This method assesses the effects of single-point variants on protein thermodynamic stability based on point mutated protein 3D structure profile. Given a protein sequence with a single variant as input, MU3DSP integrates both sequence-level features and averaged features of 3D structures obtained from sequence alignment to PDB to assess the change of thermodynamic stability induced by the substitution. MU3DSP outperforms existing methods on various benchmarks, making it a reliable tool to assess both somatic and germline substitution variants and assist in protein design. MU3DSP is available as an open-source tool at https://github.com/hurraygong/MU3DSP.
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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
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Hassabis D
影响因子：
48
作者：
Fowler, Douglas M.;Fields, Stanley
通讯作者：
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影响因子：
7.4
作者：
Kang R;Kroemer G;Tang D
通讯作者：
Tang D
影响因子：
5.8
作者：
Huang, Liang-Tsung;Gromiha, M. Michael;Ho, Shinn-Ying
通讯作者：
Ho, Shinn-Ying
影响因子：
8
作者：
Bullock, AN;Henckel, J;Fersht, AR
通讯作者：
Fersht, AR