码头6:通过预先计算的连接体构造进行分层穿越,以实现大规模的对接
Trent E Balius1, Y Stanley Tan1, Mayukh Chakrabarti1
1NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA.
我们通过添加层次数据库搜索来增强DOCK 6的分子选功能,提高速度,但略降低姿势准确性. 在DOCK 6中对接后扭力最小化最终超过了DOCK 3.7的性能.
科学领域:
- 计算化学是一种计算化学.
- 药物发现 药物发现
- 分子建模分子建模
背景情况:
- DOCK 6 是一个广泛使用的分子对接软件.
- 选大型化学库需要高效的计算方法.
- 之前的DOCK版本在探索广的化学空间方面存在局限性.
研究的目的:
- 增强DOCK 6对选前所未有的化学空间的能力.
- 将DOCK 3.7的功能集成到DOCK 6中.
- 提高虚拟选的速度和效率.
主要方法:
- 在DOCK 6中实现了层次数据库搜索程序,以跨越预先计算的连接体构造.
- 在DUDE-Z和SB2012基准数据集上测试了增强的DOCK 6.
- 将层次数据库搜索的性能与和增长方法进行了比较.
- 使用DOCK 6对2300万个碎片分子进行了大规模的虚拟屏幕.
主要成果:
- 在DOCK 6中对数据库进行分层搜索的速度是 anchor-and-grow的16倍.
- 层次数据库搜索显示,与和成长相比,实验性姿势复制减少了16%.
- 平均而言,DOCK 3.7表现出比DOCK 6更好的缩性能.
- 在没有对接后扭力最小化的情况下,DOCK 6的平均速度是DOCK 3.7的1.7倍.
- 随着对接后扭力最小化,DOCK 6的性能超过了DOCK 3.7.
结论:
- 将层次数据库搜索集成到DOCK 6中显著增加了选速度.
- 在对接后最大限度地减少扭转对于优化DOCK 6性能至关重要,使其能够超越DOCK 3.7.
- 凭借其增强的功能,DOCK 6能够大规模虚拟选庞大的化学库.
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