DOCK

{{Short description|Molecular modelling software}}

{{About|the software|the protein class|DOCK (protein)|other uses|Dock (disambiguation)}}

{{Use dmy dates|date=April 2024}}

{{Infobox software

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| author = Brian K. Shoichet, David A. Case, Robert C.Rizzo

| developer = University of California, San Francisco

| released = {{Start date and age|1982}}

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| latest release version = 3 series: 3.7; 6 series: 6.7

| latest release date = {{Start date and age|2015|02|12|df=yes}}

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| programming language = DOCK 3: Fortran, C
DOCK 6: C++, C, Fortran 77

| operating system = DOCK 3: source code
DOCK 6: Linux, macOS, Windows

| platform = x86, x86-64

| size = 100 MB

| language = English

| genre = Molecular docking

| license = Proprietary: freeware academic, commercial

| website = {{URL|dock.compbio.ucsf.edu}}

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The program UCSF DOCK was created in the 1980s by Irwin "Tack" Kuntz's Group, and was the first docking program.{{cite journal |last1= Kuntz |first1= ID |last2= Blaney |first2= JM |last3= Oatley |first3= SJ |last4= Langridge |first4= R |last5= Ferrin |first5= TE |title= A geometric approach to macromolecule-ligand interactions |journal= Journal of Molecular Biology |volume= 161 |issue= 2 |pages= 269–88 |year= 1982 |pmid= 7154081 |doi=10.1016/0022-2836(82)90153-X}} DOCK uses geometric algorithms to predict the binding modes of small molecules.{{cite journal |last1= Ewing |first1= TJ |last2= Makino |first2= S |last3= Skillman |first3= AG |last4= Kuntz |first4= ID |title= DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases |journal= Journal of Computer-aided Molecular Design |volume= 15 |issue= 5 |pages= 411–28 |year= 2001 |pmid= 11394736 |doi= 10.1023/A:1011115820450|bibcode= 2001JCAMD..15..411E |s2cid= 5553209 }}{{cite journal |last1= Moustakas |first1= DT |last2= Lang |first2= PT |last3= Pegg |first3= S |last4= Pettersen |first4= E |last5= Kuntz |first5= ID |last6= Brooijmans |first6= N |last7= Rizzo |first7= RC |title= Development and validation of a modular, extensible docking program: DOCK 5 |journal= Journal of Computer-aided Molecular Design |volume= 20 |issue= 10–11 |pages= 601–19 |year= 2006 |pmid= 17149653 |doi= 10.1007/s10822-006-9060-4|bibcode= 2006JCAMD..20..601M |s2cid= 24495648 }}{{cite journal |last1= Lang |first1= PT |last2= Brozell |first2= SR |last3= Mukherjee |first3= S |last4= Pettersen |first4= EF |last5= Meng |first5= EC |last6= Thomas |first6= V |last7= Rizzo |first7= RC |last8= Case |first8= DA |last9= James |first9= TL |last10= Kuntz |first10= I. D. |title= DOCK 6: Combining techniques to model RNA–small molecule complexes |journal= RNA |volume= 15 |issue= 6 |pages= 1219–30 |year= 2009 |pmid= 19369428 |pmc= 2685511 |doi= 10.1261/rna.1563609 |display-authors= 8}} Brian K. Shoichet, David A. Case, and Robert C.Rizzo are codevelopers of DOCK.

Two versions of the docking program are actively developed: DOCK 6 and DOCK 3.

Ligand sampling methods used by the program DOCK include.

• Rigid docking: shape matching, uses spheres placed in the pocket and performs bipartite matching between those spheres and the molecule (all versions).
• Flexible ligand is accounted for using the following methods: an algorithm called anchor and grow (v4-v6), and hierarchical docking of databases (v3.5-3.7).{{cite journal |last1= Lorber |first1= DM |last2= Shoichet |first2= BK |title =Flexible ligand docking using conformational ensembles |journal= Protein Sci |volume= 7 |issue= 4 |pages= 938–950 |year= 1998 |pmid= 9568900 |pmc= 2143983 |doi= 10.1002/pro.5560070411}}{{cite journal |last1= Lorber |first1= DM |last2= Shoichet |first2= BK |title= Hierarchical Docking of Databases of Multiple Ligand Conformations |journal= Curr Top Med Chem |volume= 5 |issue= 8 |pages= 739–49 |year= 2005 |pmid= 16101414 |doi= 10.2174/1568026054637683 |pmc= 1364474}}

A molecular dynamics engine was implemented into DOCK v6 by David A. Case's Group in the scoring function AMBER score. This ability accounts for receptor flexibility and allows for rank ordering by energetic ensembles in the docking calculations.