Molecular docking with ArgusLab An efficient shape 分子对接的一种有效的形状与ArgusLab.pptVIP

下载本文档

151
0
约8.01千字
约 24页
2017-03-08 发布于上海
举报
版权申诉

Molecular docking with ArgusLab An efficient shape 分子对接的一种有效的形状与ArgusLab.ppt

1、原创力文档（book118）网站文档一经付费（服务费），不意味着购买了该文档的版权，仅供个人/单位学习、研究之用，不得用于商业用途，未经授权，严禁复制、发行、汇编、翻译或者网络传播等，侵权必究。。
2、本站所有内容均由合作方或网友上传，本站不对文档的完整性、权威性及其观点立场正确性做任何保证或承诺！文档内容仅供研究参考，付费前请自行鉴别。如您付费，意味着您自己接受本站规则且自行承担风险，本站不退款、不进行额外附加服务；查看《如何避免下载的几个坑》。如果您已付费下载过本站文档，您可以点击这里二次下载。
3、如文档侵犯商业秘密、侵犯著作权、侵犯人身权等，请点击“版权申诉”（推荐），也可以打举报电话：400-050-0827(电话支持时间：9:00-18:30)。
4、该文档为VIP文档，如果想要下载，成为VIP会员后，下载免费。
5、成为VIP后，下载本文档将扣除1次下载权益。下载后，不支持退款、换文档。如有疑问请联系我们。
6、成为VIP后，您将拥有八大权益，权益包括：VIP文档下载权益、阅读免打扰、文档格式转换、高级专利检索、专属身份标志、高级客服、多端互通、版权登记。
7、VIP文档为合作方或网友上传，每下载1次，网站将根据用户上传文档的质量评分、类型等，对文档贡献者给予高额补贴、流量扶持。如果你也想贡献VIP文档。上传文档

Molecular docking with ArgusLab An efficient shape 分子对接的一种有效的形状与ArgusLab

GADockLamarckian Genetic Algorithm Translation Rigid-body rotation Torsions Population of individuals Fitness of each is docking score Each generation: Select breeding individuals Mutation Crossover Local minimization Elitism Check for convergence Compare GADock ShapeDock Robust General Slow, hard to define convergence Not reproducible (Stochastic) Can get caught in a local minima Some ligand/binding site types still cause problems Fast! Reproducible Formally explores all minima * * Mark Thompson Planaria Software Seattle, WA Molecular Docking With ArgusLab ·???? Find the optimal ligand/protein configurations and accurately (at least consistently) predict their binding free energy without using formal statistical mechanics approaches. ·???? Ligand is flexible. ·???? Protein binding site is flexible (side chains and protein backbone). ·???? Do this in under ~5 seconds on a commodity processor (ideally under 1 second or faster). Molecular DockingA complicated search problem We have developed two docking engines and an empirical scoring function in ArgusLab 4.0. ShapeDock: shape-based method, approximates exhaustive search. GADock: Lamarckian genetic algorithm similar to AutoDock. AScore: scoring function based on XScore of Wang and coworkers. Typical ShapeDock times for ligands with 10-15 torsions are 30 seconds on a 2.4 GHz Pentium laptop computer. ? Our docking code is implemented for both interactive docking and screening of ligand databases. Abstract Molecular modeling application runs on Windows platforms. ArgusLab 4.0 ?? 1. Ligand is described as a torsion tree Nodes are groups of bonded atoms that do not have rotatable bonds; connections between nodes are torsions. Topology of tree is crucial to efficient docking. A balanced tree with a large central node is best. ? 2. Construct two grids that overlay the binding site Grid points marked as inside or outside the free volume of binding site. Fine grid used to determine if atoms of a po