Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Bioinformatics. 2022 Feb 7;38(5):1452-1454. doi: 10.1093/bioinformatics/btab813.
Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task.
We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D.
Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar).
Supplementary data are available at Bioinformatics online.
膜蛋白约占人类基因的五分之一，但却占所有获得美国食品和药物管理局 (FDA) 批准的药物靶点的一半以上。得益于新技术的进步，PDB 中存储的膜蛋白数量迅速增加。然而，自动识别膜蛋白或推断其膜定位并不是一项简单的任务。
我们对 RCSB 蛋白质数据库网站（RCSB PDB，rcsb.org）进行了最新改进，这些改进提供了来自四个外部资源的丰富的新膜蛋白注释：OPM、PDBTM、MemProtMD 和 mpstruc。我们极大地增强了对膜蛋白数据的展示。rcsb.org 上提供注释的膜蛋白数量增加了约 80%。用户可以搜索这些注释，探索相应的树层次结构，在 1D 氨基酸序列水平上显示膜段，并在 3D 中可视化预测的膜层位置。
注释、搜索、树数据和可视化都可在我们的 rcsb.org 网站门户上获得。开源的 Mol* 查看器（molstar.org 和 github.com/molstar/molstar）支持膜可视化。
补充数据可在“Bioinformatics”在线获取。
