Reciprocal best structure hits: using AlphaFold models to discover distant homologues.
Reciprocal best structure hits: using AlphaFold models to discover distant homologues.
复制标题
DOI：
10.1093/bioadv/vbac072
复制
发表时间：
2022
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
检测同源蛋白对的常规方法使用蛋白质序列的比较。但是，两种同源蛋白的序列可能会显着分歧，因此可能无法通过标准方法进行检测。 Alphafold 2.0软件的发布可以预测高度准确的蛋白质结构，并为促进我们对蛋白质功能的理解提供了许多机会，包括检测同源蛋白质结构对。
在这项概念验证工作中，我们使用Alphafold数据库的五个模型生物的结构模型搜索最接近的同源蛋白对。我们将结果与通过其序列相似性检测到的同源蛋白对进行了比较，并表明结构匹配方法发现了一组相似的结果。此外，我们仅通过结构匹配方法检测潜在的新型同源物，这可以帮助理解未表征的蛋白质的功能，并在特征良好的蛋白质之间建立先前被忽视的连接。我们还观察到实施基于结构的方法的局限性，尤其是在处理高度无序的蛋白质或短蛋白结构时。我们的工作表明，高精度蛋白结构模型可用于发现同源蛋白质对，并且我们暴露了改善这种结构匹配方法的区域。
可以在以下URL上找到发现的同源蛋白对的信息：https：//doi.org/10.17863/cam.87873。可以在此处访问代码：https：//github.com/vivianmonzon/reciprocal_best_structure_hits。
补充数据可在在线生物信息学进步中获得。
The conventional methods to detect homologous protein pairs use the comparison of protein sequences. But the sequences of two homologous proteins may diverge significantly and consequently may be undetectable by standard approaches. The release of the AlphaFold 2.0 software enables the prediction of highly accurate protein structures and opens many opportunities to advance our understanding of protein functions, including the detection of homologous protein structure pairs. In this proof-of-concept work, we search for the closest homologous protein pairs using the structure models of five model organisms from the AlphaFold database. We compare the results with homologous protein pairs detected by their sequence similarity and show that the structural matching approach finds a similar set of results. In addition, we detect potential novel homologs solely with the structural matching approach, which can help to understand the function of uncharacterized proteins and make previously overlooked connections between well-characterized proteins. We also observe limitations of our implementation of the structure-based approach, particularly when handling highly disordered proteins or short protein structures. Our work shows that high accuracy protein structure models can be used to discover homologous protein pairs, and we expose areas for improvement of this structural matching approach. Information to the discovered homologous protein pairs can be found at the following URL: https://doi.org/10.17863/CAM.87873. The code can be accessed here: https://github.com/VivianMonzon/Reciprocal_Best_Structure_Hits. Supplementary data are available at Bioinformatics Advances online.
登录
查看更多内容
影响因子：
14.9
作者：
Mi H;Ebert D;Muruganujan A;Mills C;Albou LP;Mushayamaha T;Thomas PD
通讯作者：
Thomas PD
影响因子：
14.9
作者：
Mistry J;Chuguransky S;Williams L;Qureshi M;Salazar GA;Sonnhammer ELL;Tosatto SCE;Paladin L;Raj S;Richardson LJ;Finn RD;Bateman A
通讯作者：
Bateman A
影响因子：
64.8
作者：
Tunyasuvunakool K;Adler J;Wu Z;Green T;Zielinski M;Žídek A;Bridgland A;Cowie A;Meyer C;Laydon A;Velankar S;Kleywegt GJ;Bateman A;Evans R;Pritzel A;Figurnov M;Ronneberger O;Bates R;Kohl SAA;Potapenko A;Ballard AJ;Romera-Paredes B;Nikolov S;Jain R;Clancy E;Reiman D;Petersen S;Senior AW;Kavukcuoglu K;Birney E;Kohli P;Jumper J;Hassabis D
通讯作者：
Hassabis D
影响因子：
3.7
作者：
Nichio BTL;Marchaukoski JN;Raittz RT
通讯作者：
Raittz RT
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