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Protocols

Raccoon specifications

Information


Unique identifier OMICS_21300
Name Raccoon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.0
Stability Beta
Requirements
MGLTools, AutoDock
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Arthur J. Olson

Publication for Raccoon

Raccoon citations

 (7)
library_books

PIP3 binding proteins promote age dependent protein aggregation and limit survival in C. elegans

2016
Oncotarget
PMCID: 5226477
PMID: 27429199
DOI: 10.18632/oncotarget.10549

[…] rieved at random from the PDB database (http://www.rcsb.org). Heteroatoms (ligand), if present in downloaded structures, were manually removed before docking, as above, in AutoDock Vina 4.2 (run with Raccoon interface on a 32-core Linux cluster). To avoid bias, entire proteins were made available for docking. Grid dimensions were defined manually for each interaction. The Gibbs free energy of bind […]

call_split

1001 Ways to run AutoDock Vina for virtual screening

2016
J Comput Aided Mol Des
PMCID: 4801993
PMID: 26897747
DOI: 10.1007/s10822-016-9900-9
call_split See protocol

[…] nds (7.43 %) have 0 or 1 active torsions and only 6,872 (7.21 %) have 10 or more. In practice, however, compounds with too many rotatable bonds could be excluded from VS (for example using tools like Raccoon2), since such compounds are not expected to produce accurate results with existing docking tools. Figure  (right) shows the distribution of the compounds based on how many heavy atoms they hav […]

call_split

A novel small molecule inhibitor of HIV 1 entry

2015
Drug Des Devel Ther
PMCID: 4598220
PMID: 26491257
DOI: 10.2147/DDDT.S89338
call_split See protocol

[…] through 5,000 steps of steepest descent followed by 5,000 steps of conjugated gradient with the gaff force field. The compounds were then prepared for molecular docking calculations with the help of Raccoon software. In this step, all rotatable dihedral angles were set free to move during the calculations. Molecular docking calculations were performed with the Autodock 4.2 software. The Lamarckia […]

library_books

Identification of a Novel Drug Lead That Inhibits HCV Infection and Cell to Cell Transmission by Targeting the HCV E2 Glycoprotein

2014
PLoS One
PMCID: 4214736
PMID: 25357246
DOI: 10.1371/journal.pone.0111333

[…] t III library containing 1,715 models of compounds was obtained from the ZINC server (http://zinc.docking.org) . The multi-molecule “mol2” files from ZINC were prepared for docking calculations using Raccoon , which added the Gasteiger-Marsili charges, merged the non-polar hydrogen atoms onto their respective heavy atoms, and determined which bonds should be allowed to freely rotate during the cal […]

library_books

Exploring the Molecular Basis for Selective Binding of Homoserine Dehydrogenase from Mycobacterium leprae TN toward Inhibitors: A Virtual Screening Study

2014
Int J Mol Sci
PMCID: 3958823
PMID: 24469317
DOI: 10.3390/ijms15021826

[…] e was employed. The target used in our study was the 3D structure of HSD mentioned above. Modification and format conversion of compounds which were downloaded from NPD used Open Babel toolbox [] and Raccoon [] graphical user interface for AutoDock [,] with a special focus on large-scale virtual screening.There are 22 atom types in the docking course. The Parameters are listed as follow: ga_num_ev […]

library_books

Mycoplasmosis in Ferrets

2012
PMCID: 3559160
PMID: 23092744
DOI: 10.3201/eid1811.120072

[…] ral cavities of 81% of clinically healthy ferrets kept in a laboratory setting (). This mycoplasma isolate was not antigenically related to any reference strains from dogs, cats, sheep, cattle, mice, raccoon dogs, or a Japanese badger. In 1983, similarly fast-growing, glucose-fermenting mycoplasmas were isolated from the lungs of healthy mink kits (1–2 months of age) in Denmark (). This species wa […]

Citations

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Raccoon institution(s)
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
Raccoon funding source(s)
Supported by grant R01 GM069832 from the National Institutes of Health.

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