Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Nucleic Acids Res. 2024 Jul 5;52(W1):W348-W353. doi: 10.1093/nar/gkae259.
Alignment of 3D molecular structures involves overlaying their sets of atoms in space in such a way as to minimize the distance between the corresponding atoms. The purpose of this procedure is usually to analyze and assess structural similarity on a global (e.g. evaluating predicted 3D models and clustering structures) or a local level (e.g. searching for common substructures). Although the idea of alignment is simple, combinatorial algorithms that implement it require considerable computational resources, even when processing relatively small structures. In this paper, we introduce RNAhugs, a web server for custom and flexible alignment of 3D RNA structures. Using two efficient heuristics, GEOS and GENS, it finds the longest corresponding fragments within 3D structures that may differ in sizes-given in the PDB or PDBx/mmCIF formats-that manage to align with user-specified accuracy (i.e. with an RMSD not exceeding a cutoff value given as an input parameter). A distinctive advantage of the system lies in its ability to process multi-model files and compare the results of 1-25 alignments in a single task. RNAhugs has an intuitive interface and is publicly available at https://rnahugs.cs.put.poznan.pl/.
3D 分子结构的对齐涉及到将其原子集在空间中进行叠加，以使相应原子之间的距离最小化。该过程的目的通常是在全局（例如，评估预测的 3D 模型和聚类结构）或局部（例如，搜索公共子结构）级别上分析和评估结构相似性。尽管对齐的想法很简单，但实现它的组合算法需要相当大的计算资源，即使在处理相对较小的结构时也是如此。在本文中，我们介绍了 RNAhugs，这是一个用于定制和灵活对齐 3D RNA 结构的网络服务器。它使用两种有效的启发式算法 GEOS 和 GENS，在可能在大小上有所不同的 3D 结构（以 PDB 或 PDBx/mmCIF 格式给出）中找到最长的相应片段，这些片段设法以用户指定的精度对齐（即 RMSD 不超过作为输入参数给出的截止值）。该系统的一个显著优势在于它能够处理多模型文件，并在单个任务中比较 1-25 次对齐的结果。RNAhugs 具有直观的界面，并可在 https://rnahugs.cs.put.poznan.pl/ 上公开获得。
