基于 FFT 采样的蛋白质配体对接：D3R 案例研究。
Protein-ligand docking using FFT based sampling: D3R case study.
机构信息
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11794, USA.
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
出版信息
J Comput Aided Mol Des. 2018 Jan;32(1):225-230. doi: 10.1007/s10822-017-0069-7. Epub 2017 Nov 3.
Abstract
Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein-ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein-ligand interaction landscape, which will be explored in further applications.
摘要
基于快速傅里叶变换（FFT）的方法已成功应用于相对刚性的蛋白质-蛋白质复合物的建模。最近，我们已经能够将 FFT 方法应用于柔性蛋白质-肽相互作用的处理。在这里，我们报告了我们最新的尝试，即将 FFT 方法的功能扩展到处理应用于 D3R PL-2016-1 挑战的柔性蛋白质-配体相互作用。基于 D3R 的评估，我们的 FFT 方法与蒙特卡罗非网格细化最小化相结合，是挑战中表现最好的方法之一。我们的方法的潜在优势在于其能够全局采样蛋白质-配体相互作用景观，这将在进一步的应用中进行探索。
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