DOCK

DOCK
原作者	Brian K. Shoichet; David A. Case; Robert C.Rizzo
開發者	加州大学旧金山分校
首次发布	1982年，42年前
当前版本	DOCK 3：3.8; DOCK 6：6.12
编程语言	DOCK 3：Fortran、C语言; DOCK 6：C++、C语言、Fortran 77
操作系统	DOCK 3：源代码; DOCK 6：Linux、macOS、Windows
平台	x86、x86-64
文件大小	100 MB
语言	英语
类型	分子对接（英语：docking (molecular)）
许可协议	专有: ; 对学术机构免费; 对行业组织收费
网站	dock.compbio.ucsf.edu
数据截至	2024-10-04

UCSF DOCK是由欧文“塔克”孔茨（英语：Irwin "Tack" Kuntz）小组于20世纪80年代开发的首个分子对接程序。^[1]DOCK使用几何算法来预测小分子的结合模式。^[2]^[3]^[4] 布赖恩·肖切特（Brian K. Shoichet）、戴维·凯斯（David A. Case）、罗伯特·里佐（Robert C.Rizzo）是该软件的开发者。

小组目前正在开发DOCK 3和DOCK 6两个版本的程序。

DOCK使用的配体采样方法包括：

刚性对接：形状匹配，使用放置在袋中的微球并对这些微球和分子进行二分图匹配（所有版本）。
自由配体使用锚点和增长算法（DOCK 4-6）^[5]、数据库的层次对接（DOCK3.5-3.8）进行计算。^[6]^[7]

戴维·凯斯小组在DOCK 6的打分函数AMBER score中加入了分子动力学引擎。这一功能考虑到了受体的灵活性，并允许在分子对接计算中按含能集成排序。^[8]

参见

AutoDock（英语：AutoDock）
分子建模
分子力学建模软件比较（英语：Comparison of software for molecular mechanics modeling）

参考资料

^ Kuntz, ID; Blaney, JM; Oatley, SJ; Langridge, R; Ferrin, TE. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology. 1982, 161 (2): 269–88. PMID 7154081. doi:10.1016/0022-2836(82)90153-X.
^ Ewing, TJ; Makino, S; Skillman, AG; Kuntz, ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. Journal of Computer-aided Molecular Design. 2001, 15 (5): 411–28. Bibcode:2001JCAMD..15..411E. PMID 11394736. S2CID 5553209. doi:10.1023/A:1011115820450.
^ Moustakas, DT; Lang, PT; Pegg, S; Pettersen, E; Kuntz, ID; Brooijmans, N; Rizzo, RC. Development and validation of a modular, extensible docking program: DOCK 5. Journal of Computer-aided Molecular Design. 2006, 20 (10–11): 601–19. Bibcode:2006JCAMD..20..601M. PMID 17149653. S2CID 24495648. doi:10.1007/s10822-006-9060-4.
^ Lang, PT; Brozell, SR; Mukherjee, S; Pettersen, EF; Meng, EC; Thomas, V; Rizzo, RC; Case, DA; et al. DOCK 6: Combining techniques to model RNA–small molecule complexes. RNA. 2009, 15 (6): 1219–30. PMC 2685511 . PMID 19369428. doi:10.1261/rna.1563609.
^ Ewing, TJ; Makino, S; Skillman, AG; Kuntz, ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. Journal of Computer-aided Molecular Design. 2001, 15 (5): 411–28. Bibcode:2001JCAMD..15..411E. PMID 11394736. S2CID 5553209. doi:10.1023/A:1011115820450.
^ Lorber, DM; Shoichet, BK. Flexible ligand docking using conformational ensembles. Protein Sci. 1998, 7 (4): 938–950. PMC 2143983 . PMID 9568900. doi:10.1002/pro.5560070411.
^ Lorber, DM; Shoichet, BK. Hierarchical Docking of Databases of Multiple Ligand Conformations. Curr Top Med Chem. 2005, 5 (8): 739–49. PMC 1364474 . PMID 16101414. doi:10.2174/1568026054637683.
^ Lang, PT; Brozell, SR; Mukherjee, S; Pettersen, EF; Meng, EC; Thomas, V; Rizzo, RC; Case, DA; et al. DOCK 6: Combining techniques to model RNA–small molecule complexes. RNA. 2009, 15 (6): 1219–30. PMC 2685511 . PMID 19369428. doi:10.1261/rna.1563609.

外部链接

UCSF DOCK官方网站

[DOCK-1] Kuntz, ID; Blaney, JM; Oatley, SJ; Langridge, R; Ferrin, TE. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology. 1982, 161 (2): 269–88. PMID 7154081. doi:10.1016/0022-2836(82)90153-X.

[DOCK4-2] Ewing, TJ; Makino, S; Skillman, AG; Kuntz, ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. Journal of Computer-aided Molecular Design. 2001, 15 (5): 411–28. Bibcode:2001JCAMD..15..411E. PMID 11394736. S2CID 5553209. doi:10.1023/A:1011115820450.

[3] Moustakas, DT; Lang, PT; Pegg, S; Pettersen, E; Kuntz, ID; Brooijmans, N; Rizzo, RC. Development and validation of a modular, extensible docking program: DOCK 5. Journal of Computer-aided Molecular Design. 2006, 20 (10–11): 601–19. Bibcode:2006JCAMD..20..601M. PMID 17149653. S2CID 24495648. doi:10.1007/s10822-006-9060-4.

[DOCK6-4] Lang, PT; Brozell, SR; Mukherjee, S; Pettersen, EF; Meng, EC; Thomas, V; Rizzo, RC; Case, DA; et al. DOCK 6: Combining techniques to model RNA–small molecule complexes. RNA. 2009, 15 (6): 1219–30. PMC 2685511 . PMID 19369428. doi:10.1261/rna.1563609.

[DOCK4_2-5] Ewing, TJ; Makino, S; Skillman, AG; Kuntz, ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. Journal of Computer-aided Molecular Design. 2001, 15 (5): 411–28. Bibcode:2001JCAMD..15..411E. PMID 11394736. S2CID 5553209. doi:10.1023/A:1011115820450.

[DOCK3.5-6] Lorber, DM; Shoichet, BK. Flexible ligand docking using conformational ensembles. Protein Sci. 1998, 7 (4): 938–950. PMC 2143983 . PMID 9568900. doi:10.1002/pro.5560070411.

[DOCK3.5HD-7] Lorber, DM; Shoichet, BK. Hierarchical Docking of Databases of Multiple Ligand Conformations. Curr Top Med Chem. 2005, 5 (8): 739–49. PMC 1364474 . PMID 16101414. doi:10.2174/1568026054637683.

[DOCK6_2-8] Lang, PT; Brozell, SR; Mukherjee, S; Pettersen, EF; Meng, EC; Thomas, V; Rizzo, RC; Case, DA; et al. DOCK 6: Combining techniques to model RNA–small molecule complexes. RNA. 2009, 15 (6): 1219–30. PMC 2685511 . PMID 19369428. doi:10.1261/rna.1563609.

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