利用蛋白质块从蛋白质结构构建定制片段库
Using protein blocks to build custom fragment libraries from protein structures
AI总结：
本文提出利用蛋白质块（PBs）将三维结构编码为一维序列，结合PB-ALIGN和PB-kPRED工具及新评分函数，从非冗余结构数据库中高效构建覆盖超70%局部主链的高质量定制片段库。
摘要：
现代蛋白质显著的结构多样性反映了数百万年的进化过程，在这一过程中序列空间不断扩展，而许多结构特征仍然保持保守。这种保守性不仅在同源蛋白质中显而易见，也体现在超二级基序在不相关蛋白质中的反复出现上，凸显了这些结构单元的丰富性和稳健性。在此，我们提出了一种新的流程，利用蛋白质块（PBs）——一种编码局部主链构象的结构字母表——来生成定制化的蛋白质片段库。我们的方法通过将三维结构转换为一维PB序列，从经过整理的非冗余蛋白质结构数据库中高效提取结构相似的片段。通过将预测的PB序列与PB-ALIGN和PB-kPRED工具相结合，我们的方法能够独立于序列同源性来识别相关片段。片段质量进一步通过一个新的评分函数进行评估，该函数结合了二级结构相似性和PB比对指标。所得片段库包含至少七个PB（11个氨基酸残基）的片段，覆盖了超过70%的局部主链结构。我们的结果表明，PB能够从多样化的蛋白质空间中高效挖掘高质量的结构片段，包括具有无序区域的蛋白质。该流程可作为在线工具使用（PB-Frag，https://pbpred-us2b.univ-nantes.fr/pbfrag）。
英文摘要：
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous proteins but also in the recurrence of supersecondary motifs across unrelated proteins, underscoring the abundance and robustness of these structural units. Here, we present a novel pipeline for generating customized protein fragment libraries using protein blocks (PBs) - a structural alphabet that encodes local backbone conformations. Our method efficiently extracts structurally similar fragments from a curated, non-redundant protein structure database by converting three-dimensional structures into one-dimensional PB sequences. By integrating predicted PB sequences with the PB-ALIGN and PB-kPRED tools, our approach identifies relevant fragments independently of sequence homology. Fragment quality is further assessed using a new scoring function that combines secondary structure similarity and PB alignment metrics. The resulting libraries contain fragments of at least seven PBs (11 amino acid residues), covering over 70% of the local backbone structure. Our results demonstrate that PBs enable efficient mining of high-quality structural fragments from diverse protein spaces, including proteins with disordered regions. The pipeline is accessible as an online tool (PB-Frag, https://pbpred-us2b.univ-nantes.fr/pbfrag ).
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
