The PDock suite is a software package for performing molecular docking simulations. PDock was designed to bea modular and extensible software package that interfaces easily with third party codes to quickly evaluate and test different methods for moleuclar docking simulations. Docking calculations start with three dimensional atomistic models of two molecules (usually a protein and small molecule) and predict how they will bind to each other. This problem can be broken down into 2 main steps: 1) predicting various orientation/conformation combinations (called 'poses') of one molecule to "dock" into the other one and 2) scoring each possible pose. The best scoring pose is predicted to be the biological one. PDock has two main algoritms for performing the first step of docking. The first performs a biased search of poses using its own implementation of the published DOCK algorithm. The second is an evolutionary search algorithm. PDock uses a force-field based scoring scheme with an option of perform a more computationally expensive solvation correction. The PDock suite includes the following programs : PDock (main program); PGrid: for pre-processing input files; ProteinPDock (simplified main ()and input file for special case of protein-protein docking); and CombiPDock (simpliefied main() and input file for special case of combinatorial libraries).
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@misc{osti_1230959,
title = {PDock Suite, Version 00},
author = {Roe, Diana},
abstractNote = {The PDock suite is a software package for performing molecular docking simulations. PDock was designed to bea modular and extensible software package that interfaces easily with third party codes to quickly evaluate and test different methods for moleuclar docking simulations. Docking calculations start with three dimensional atomistic models of two molecules (usually a protein and small molecule) and predict how they will bind to each other. This problem can be broken down into 2 main steps: 1) predicting various orientation/conformation combinations (called 'poses') of one molecule to "dock" into the other one and 2) scoring each possible pose. The best scoring pose is predicted to be the biological one. PDock has two main algoritms for performing the first step of docking. The first performs a biased search of poses using its own implementation of the published DOCK algorithm. The second is an evolutionary search algorithm. PDock uses a force-field based scoring scheme with an option of perform a more computationally expensive solvation correction. The PDock suite includes the following programs : PDock (main program); PGrid: for pre-processing input files; ProteinPDock (simplified main ()and input file for special case of protein-protein docking); and CombiPDock (simpliefied main() and input file for special case of combinatorial libraries).},
doi = {},
url = {https://www.osti.gov/biblio/1230959},
year = {Thu Mar 01 00:00:00 EST 2007},
month = {Thu Mar 01 00:00:00 EST 2007},
note =
}
