BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.
BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.
复制标题
BCL：：Conf：使用晶体学开放数据库改进的基于知识的开源构象采样。
DOI：
10.1021/acs.jcim.0c01140
复制
发表时间：
2021-01-25
影响因子：
5.6
通讯作者：
Meiler J
中科院分区：
文献类型：
--
作者：
Mendenhall J;Brown BP;Kothiwale S;Meiler J
BCL::Conf是一种基于知识的构象采样算法，利用来自剑桥结构数据库（CSD，需要许可）的小分子片段旋转体库，作为生化库（BCL）化学信息学工具包的一个组成部分。本文描述了对BCL::Conf算法所做的实质性改进，并过渡到从Crystallography Open Database （COD，无需许可）中的分子派生的rotamer库。我们证明了新的BCL::Conf在高质量蛋白质配体复合物的白金数据集中对天然构象恢复的性能。这组2859个结构先前已被用于评估十几种构象生成算法的性能，包括Conformator、Balloon、RDKit DG、ETKDG、Confab、Frog2、MultiConf-DOCK、CSD构象生成器、ConfGenX-OPSL3力场、Omega、excalc、iCon和MOE。这些基准测试表明，CSD一致性生成器处于报告的一致性生成器的最先进状态。我们的研究结果表明，改进的BCL::Conf在一系列集成大小的结合一致性恢复方面明显优于CSD一致性生成算法，并且具有相似的快速一致性生成速率。BCL::Conf现在与派生于cod的rotamer库一起发布，并且可以免费用于学术用途。BCL可以从http://meilerlab.org/bclcommons下载，适用于Windows、Linux或Apple操作系统。BCL::Conf现在也可以通过web服务器访问http://meilerlab.org/bclconf。
We previously described BCL::Conf, a knowledge-based conformation sampling algorithm utilizing a small molecule fragment rotamer library derived from the Cambridge Structural Database (CSD, license required), as a component of the BioChemical Library (BCL) cheminformatics toolkit. This paper describes substantial improvements made to the BCL::Conf algorithm and a transition to a rotamer library derived from molecules in the Crystallography Open Database (COD, no license required). We demonstrate the performance of the new BCL::Conf on native conformer recovery in the Platinum dataset of high-quality protein-ligand complexes. This set of 2859 structures has previously been used to assess the performance of over a dozen conformer generation algorithms, including the Conformator, Balloon, RDKit DG, ETKDG, Confab, Frog2, MultiConf-DOCK, CSD conformer generator, ConfGenX-OPSL3 force field, Omega, excalc, iCon, and MOE. These benchmarks suggest that the CSD conformer generator is at the state of the art of reported conformer generators. Our results indicate that the improved BCL::Conf significantly outperforms the CSD conformer generation algorithm at binding conformer recovery across a range of ensemble sizes and with similarly fast rates of conformer generation. BCL::Conf is now distributed with the COD-derived rotamer library and is free for academic use. The BCL can be downloaded at http://meilerlab.org/bclcommons for Windows, Linux, or Apple operating systems. BCL::Conf can now also be accessed via webserver at http://meilerlab.org/bclconf.
登录
查看更多内容
影响因子：
3.7
作者：
DeLuca S;Khar K;Meiler J
通讯作者：
Meiler J
影响因子：
5.6
作者：
Friedrich, Nils-Ole;Meyder, Agnes;Kirchmair, Johannes
通讯作者：
Kirchmair, Johannes
影响因子：
5.6
作者：
Friedrich, Nils-Ole, V;Flachsenberg, Florian;Rarey, Matthias
通讯作者：
Rarey, Matthias
影响因子：
6.1
作者：
Gražulis S;Chateigner D;Downs RT;Yokochi AF;Quirós M;Lutterotti L;Manakova E;Butkus J;Moeck P;Le Bail A
通讯作者：
Le Bail A
影响因子：
3
作者：
Iino, Daisuke;Takakura, Yasuaki;Yajima, Shunsuke
通讯作者：
Yajima, Shunsuke