DOCK

DOCK
原作者	Brian K. Shoichet; David A. Case; Robert C.Rizzo
開發者	加州大學三藩市分校
首次發佈	1982年，42年前
當前版本	DOCK 3：3.8; DOCK 6：6.12
程式語言	DOCK 3：Fortran、C語言; DOCK 6：C++、C語言、Fortran 77
作業系統	DOCK 3：原始碼; DOCK 6：Linux、macOS、Windows
平台	x86、x86-64
文件大小	100 MB
語言	英語
類型	分子對接（英語：docking (molecular)）
許可協議	專有: ; 對學術機構免費; 對行業組織收費
網站	dock.compbio.ucsf.edu
數據截至	2024-10-04

UCSF DOCK是由歐文「塔克」孔茨（英語：Irwin "Tack" Kuntz）小組於20世紀80年代開發的首個分子對接程序。^[1]DOCK使用幾何算法來預測小分子的結合模式。^[2]^[3]^[4] 布賴恩·肖切特（Brian K. Shoichet）、戴維·凱斯（David A. Case）、羅伯特·里佐（Robert C.Rizzo）是該軟件的開發者。

小組目前正在開發DOCK 3和DOCK 6兩個版本的程序。

DOCK使用的配體採樣方法包括：

剛性對接：形狀匹配，使用放置在袋中的微球並對這些微球和分子進行二分圖匹配（所有版本）。
自由配體使用錨點和增長算法（DOCK 4-6）^[5]、數據庫的層次對接（DOCK3.5-3.8）進行計算。^[6]^[7]

戴維·凱斯小組在DOCK 6的打分函數AMBER score中加入了分子動力學引擎。這一功能考慮到了受體的靈活性，並允許在分子對接計算中按含能集成排序。^[8]

參見

AutoDock（英語：AutoDock）
分子建模
分子力學建模軟件比較（英語：Comparison of software for molecular mechanics modeling）

參考資料

^ 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.

外部連結

UCSF DOCK官方網站

[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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