使用灵活的XML协议进行Rosetta配体对接。
Rosetta Ligand docking with flexible XML protocols.
作者信息
Lemmon Gordon, Meiler Jens
机构信息
Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
出版信息
Methods Mol Biol. 2012;819:143-55. doi: 10.1007/978-1-61779-465-0_10.
Abstract
RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.
摘要
RosettaLigand是用于预测蛋白质与小分子如何相互作用的一流软件。基准研究表明，RosettaLigand预测的得分最高的界面中有70%与晶体结构的RMSD在2Å以内[1]。Rosetta Ligand软件的最新版本包含许多新功能，例如：（1）同时对接多个配体；（2）将配体表示为片段以提高灵活性；（3）对接过程中对界面进行重新设计；（4）基于XML脚本的界面，让用户能够完全控制配体对接协议。
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