Institute of Computing Science & 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.
BMC Bioinformatics. 2018 Aug 22;19(1):304. doi: 10.1186/s12859-018-2317-9.
Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complement them. Recently, researchers' interests have directed towards in silico methods to fit, remodel and refine RNA tertiary structure models. Their power lies in a problem-specific exploration of RNA conformational space and efficient optimization procedures. The aim is to improve the accuracy of models obtained either computationally or experimentally.
Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/ CONCLUSIONS: RNAfitme has been applied in various RNA 3D remodeling scenarios for several types of input data. Computational experiments proved its efficiency, accuracy, and usefulness in the processing of RNAs of any size. Fidelity of RNAfitme predictions has been thoroughly tested for RNA 3D structures determined experimentally and modeled in silico.
计算 RNA 三维结构预测和建模作为确定结构的高分辨率实验技术的补充方法正在兴起。它们通常用于替代或补充这些方法。最近，研究人员的兴趣已经转向计算方法，以适应、改造和完善 RNA 三级结构模型。它们的优势在于针对 RNA 构象空间的特定问题探索和有效的优化程序。其目的是提高通过计算或实验获得的模型的准确性。
在这里，我们介绍了 RNAfitme，这是一个用于固定骨架 RNA 3D 结构中核碱基和核苷残基构象改造的多功能网络服务器工具。我们的方法利用了专门的库来定义 RNA 构象空间。这些库是基于 PDB 中已提交的 RNA 结构的扭转角特征构建的。RNAfitme 可用于从其骨架重建 RNA 的全原子模型；改造给定 RNA 结构中用户选择的核碱基/核苷残基；根据序列和相同大小同源分子的模板预测 RNA 3D 结构；通过减少结构质量评估期间指出的空间冲突来优化 RNA 3D 模型。RNAfitme 是一个具有直观界面的公共可用工具。它可在 http://rnafitme.cs.put.poznan.pl/ 免费获得。
RNAfitme 已在各种 RNA 3D 改造场景中应用于多种类型的输入数据。计算实验证明了其在处理任何大小的 RNA 方面的效率、准确性和实用性。RNAfitme 对实验确定的和计算建模的 RNA 3D 结构的预测准确性进行了彻底测试。
