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|Interface||Command line interface|
|Restrictions to use||None|
|Programming languages||C, C++|
|License||GNU General Public License version 3.0|
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Publication for ParaDockS
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
[…] 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 […]
Lestaurtinib Inhibits Histone Phosphorylation and Androgen Dependent Gene Expression in Prostate Cancer Cells
[…] 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 […]
Masitinib (AB1010), a Potent and Selective Tyrosine Kinase Inhibitor Targeting KIT
[…] 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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