Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Methods. 2013 Mar;59(3):372-81. doi: 10.1016/j.ymeth.2012.12.004. Epub 2012 Dec 23.
High-resolution structural information is needed in order to unveil the underlying mechanistic of biomolecular function. Due to the technical limitations or the nature of the underlying complexes, acquiring atomic resolution information is difficult for many challenging systems, while, often, low-resolution biochemical or biophysical data can still be obtained. To make best use of all the available information and shed light on these challenging systems, integrative computational tools are required that can judiciously combine and accurately translate sparse experimental data into structural information. In this review we discuss the current state of integrative approaches, the challenges they are confronting and the advances made regarding those challenges. Recent developments are underpinned by noteworthy application examples taken from the literature. Within this context, we also position our data-driven docking approach, HADDOCK that can integrate a variety of information sources to drive the modeling of biomolecular complexes. Only a synergistic combination of experiment and modeling will allow us to tackle the challenges of adding the structural dimension to interactomes, shed "atomic" light onto molecular processes and understand the underlying mechanistic of biomolecular function. The current state of integrative approaches indicates that they are poised to take those challenges.
为了揭示生物分子功能的基础机制,需要高分辨率的结构信息。由于技术限制或基础复合物的性质,对于许多具有挑战性的系统来说,获取原子分辨率的信息是困难的,而通常情况下,仍可以获得低分辨率的生化或生物物理数据。为了充分利用所有可用的信息,并阐明这些具有挑战性的系统,需要集成计算工具,这些工具可以明智地组合并准确地将稀疏的实验数据转化为结构信息。在这篇综述中,我们讨论了整合方法的现状、它们所面临的挑战以及在这些挑战方面取得的进展。最近的发展得到了文献中值得注意的应用实例的支持。在这方面,我们还介绍了我们的数据驱动对接方法 HADDOCK,它可以整合各种信息来源来驱动生物分子复合物的建模。只有实验和建模的协同结合,才能使我们能够解决将结构维度添加到互作组中的挑战,为分子过程带来“原子”级的光照,并理解生物分子功能的基础机制。整合方法的现状表明,它们已经准备好迎接这些挑战。