PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode
PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode
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DOI：
10.1002/pro.3320
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发表时间：
2018-01-01
期刊：
影响因子：
8
通讯作者：
Keating, Amy E.
中科院分区：
文献类型：
--
作者：
Frappier, Vincent;Duran, Madeleine;Keating, Amy E.
PixelDB，肽外域定位数据库，编译了1966个非冗余的，高分辨率的蛋白质-肽复合物的结构，过滤以最小化晶体包装对肽构象的影响。该数据库的组织是为了促进蛋白质-肽接合的结构保守与非保守元素的研究。PixelDB簇基于肽结合蛋白的结构相似性，通过比较簇内的复合物，突出了使用多种结合模式参与肽的结构域的例子。PixelDB还确定了每种结合模式的保守肽核心结构基序特征。核心基序侧面的肽区经常与我们称为外源位点的蛋白质表面发生非结构保守的相互作用。许多例子表明，外源接触对增强蛋白质结合和相互作用特异性很重要。PixelDB为计算和结构生物学家提供了研究、建模和预测核心-基序和外源位点接触肽相互作用的资源。PixelDB以方便的平面文件格式和附带的可视化工具不受限制地提供给社区。
PixelDB, the Peptide Exosite Location Database, compiles 1966 non-redundant, high-resolution structures of protein-peptide complexes filtered to minimize the impact of crystal packing on peptide conformation. The database is organized to facilitate study of structurally conserved versus non-conserved elements of protein-peptide engagement. PixelDB clusters complexes based on the structural similarity of the peptide-binding protein, and by comparing complexes within a cluster highlights examples of domains that engage peptides using more than one binding mode. PixelDB also identifies conserved peptide core structural motifs characteristic of each binding mode. Peptide regions that flank core motifs often make non-structurally conserved interactions with the protein surface in regions we call exosites. Many examples establish that exosite contacts can be important for enhancing protein binding and interaction specificity. PixelDB provides a resource for computational and structural biologists to study, model, and predict core-motif and exosite-contacting peptide interactions. PixelDB is available to the community without restriction in a convenient flat-file format with accompanying visualization tools.