Totrov Maxim
Molsoft LLC, 3366 N Torrey Pines Ct., Ste. 300, La Jolla CA 92037, USA.
Chem Biol Drug Des. 2008 Jan;71(1):15-27. doi: 10.1111/j.1747-0285.2007.00605.x. Epub 2007 Dec 7.
The atomic property fields (APF) concept is introduced as a continuous, multi-component 3D potential that reflects preferences for various atomic properties at each point in space. Atomic property field-based approaches to several key problems in the field of ligand structure-based rational drug discovery and design are investigated. The superposition of ligands on one or multiple molecular templates is performed by Monte-Carlo minimization in the atomic property fields potentials combined with standard force-field energy. The approach is extended to multiple flexible ligand alignments using an iterative procedure, Self-Consistent atomic Property Fields by Optimization (SCAPFOld). The application of atomic property fields and SCAPFOld for virtual ligand screening and 3D Quantitive Structure-Activity Relationship (QSAR) is tested on published benchmarks. The new methods are shown to perform competitively in comparison to current state-of-the-art methods.
原子性质场（APF）概念被引入作为一种连续的、多组分三维势，它反映了空间中每个点对各种原子性质的偏好。研究了基于原子性质场的方法在基于配体结构的合理药物发现与设计领域中几个关键问题上的应用。通过在原子性质场势中结合标准力场能量的蒙特卡罗最小化方法，将配体叠加到一个或多个分子模板上。该方法通过一种迭代程序——优化自洽原子性质场（SCAPFOld）扩展到多个柔性配体比对。在已发表的基准测试中，测试了原子性质场和SCAPFOld在虚拟配体筛选和三维定量构效关系（QSAR）中的应用。结果表明，与当前最先进的方法相比，新方法具有竞争力。
