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Protocols

ParaDockS specifications

Information


Unique identifier OMICS_23899
Name ParaDockS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.1.1
Stability Stable
Maintained Yes

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Publication for ParaDockS

ParaDockS citations

 (3)
library_books

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

2017
J Comput Aided Mol Des
PMCID: 5767202
PMID: 28889350
DOI: 10.1007/s10822-017-0055-0

[…] mber Force Field (GAFF) [] and AM1-BCC QM potential [], and this full topology generation was run automatically and converted to GROMACS format using ACPYPE (Rev: 7828) []. Docking was carried out by ParaDockS 1.0.1 [] with a docking radius of 1.0 nm and the docking center set to the center-of-mass coordinates of co-crystallized ligands. Representative docked ligand conformations used as input str […]

library_books

Lestaurtinib Inhibits Histone Phosphorylation and Androgen Dependent Gene Expression in Prostate Cancer Cells

2012
PLoS One
PMCID: 3332061
PMID: 22532837
DOI: 10.1371/journal.pone.0034973

[…] nsus score based on a variety of different scoring methods , . In the present study, we also calculated a consensus score using the five normalized scoring functions Chemscore, Goldscore, Glidescore, ParaDockS p-score and GBSA score. Using the consensus scoring, a clear discrimination between the highly active inhibitors staurosporine (Score 9.23) and Ro318220 (Score 9.51) and the inactive compoun […]

call_split

Masitinib (AB1010), a Potent and Selective Tyrosine Kinase Inhibitor Targeting KIT

2009
PLoS One
PMCID: 2746281
PMID: 19789626
DOI: 10.1371/journal.pone.0007258
call_split See protocol

[…] X-ray coordinates of the STI571/ABL (1IEP.pdb) and STI571/KIT (1T46.pdb) X-ray structures were taken from the Protein Databank and used in combination with our in-house docking program, ParaDocks, and the X-Score of Wang et al. to dock masitinib into ABL and KIT. Figures were prepared with PyMOL version 1.00 (DeLano Scientific). […]

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ParaDockS institution(s)
Department of Pharmaceutical Chemistry, Martin-Luther Universitat Halle-Wittenberg, Halle/Saale, Germany; Research Center Pharmaceutical Engineering GmbH, Graz, Austria; Biotechnologisches Zentrum der TU Dresden, Dresden, Germany; CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany

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