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AutoLigand specifications


Unique identifier OMICS_12386
Name AutoLigand
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Medium
Stability Stable
Maintained Yes


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  • person_outline David S. Goodsell <>

Publication for AutoLigand

AutoLigand in publications

PMCID: 5580956
PMID: 28894629
DOI: 10.5455/jice.20170709031835

[…] the streamlined protein was used as possibly permitted structure for virtual screening and docking simulations., moreover, to portray the potential dynamic site in prepared protein, we utilized autoligand module implicit in autodock tools. by applying autodock force fields, habilitated pocket was generated for binding of ligands []. pocket grid was generated using autogrid module and grid […]

PMCID: 4381396
PMID: 25888251
DOI: 10.1186/s12859-015-0518-z

[…] while dock uses grid []. as far as we know, there is no study in binding site identification based on grid []. by contrast, autogrid is used by two successful probe-mapping/energy-based algorithms; autoligand [] and sitehound []. advina docking scores were the most favorable at the as, and permitted to better discriminate it against bs2 for both targets. conversely, dock scores were not able […]

PMCID: 4217716
PMID: 25365309
DOI: 10.1371/journal.pone.0109185

[…] we used pharmmapper server to predict breast cancer target proteins for mcdf. search results showed crystal structure of the antagonist form of glucocorticoid receptor with highest fit score and autoligand analysis showed two potential binding sites, site-a and site-b for mcdf. a molecular docking was performed on these two sites and based on binding energy site-b was selected. md simulation […]

PMCID: 3546658
PMID: 23443090
DOI: 10.3390/ijms131215724

[…] binding energy. the dehd coordinate file was edited by removing the water molecules, adding hydrogen and merging nonpolar hydrogen. kolmann and gasteiger charges were added on to the structure. autoligand was allowed for 10 runs to obtain favorable local minima. the active site residues were specified. ligands (d-2cp, d-2bp, mca, mba, 2,2-dcp, d,l-2,3-dcp, 3-cp and water molecule) were also […]

PMCID: 3201956
PMID: 22046245
DOI: 10.1371/journal.pone.0025711

[…] 7 comprising pocket p3 has been shown to undergo correlated motions with the active site , , ., in addition to fragment based mapping we employed grid energy based pocket identification with the autoligand package . autoligand searches the exterior surface space of a protein for contiguous volume envelopes with potentially favorable interaction energies for small molecules. applying […]

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AutoLigand institution(s)
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
AutoLigand funding source(s)
This work was performed with support from grants R24-CA095830 and R01-GM069832 from the NIH.

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