Search Results for "autodock"

PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes...

the ADFRsuite provides a self contain python-based software environment with various tools for automated docking. visit ccsb.scripps.edu/adfr for more info

...These notebooks are Python 3 compatible. Each protocol and Jupyter notebook has its own test folder for testing and reproducibility evaluation. For all notebooks, the demonstration includes the use of AutoDock Vina and Ledock. When available, some alternatives are mentioned in the protocol. Jupyter Dock's initial goal was to provide a set of pythonic protocols for molecular docking. Nonetheless, there is a dearth of docking tools in Python for all of the steps and protocols (i.e. pocket search for blind docking). Furthermore, the majority of well-known and widely used molecular docking software have been developed as stand-alone executables or as components of software suites.

...Its success rate is higher than AutoDock Vina, but similar to AutoDockFR. https://cbbio.online/software/gwovina/index.html

A fast docking tool based on the efficient optimization algorithm of Particle Swarm Intelligence and the framework of AutoDock Vina. Based on the initial PSO implementation, our PSOVina method has undergone several important improvements to enhance the docking accuary and achieve remarkable efficiency as compared to the original AutoDock Vina. https://cbbio.online/software/psovina/index.html

DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

Utilizing opensource code of AutoDock Vina 1.1.2 by Dr. Oleg Trott, a working binaries for vina and vina_split are provided. These files can be helpful to those who are not very familiar with building source codes on Linux machines. Since the original compilation of vina stopped working after some system configuration changes on a supercomputer, I had to solve the problem by building the program from the source code.

AUDocker is a GUI for AutoDock Vina.. helps in virtual screening of huge number of ligands continuously. Helps in resumption of work in accidental shutdowns..

...We have integrated Ligand Based Virtual Screening (LBVS) technique which uses ChemmineR - a reliable cheminformatics package on R platform and Structure Based Virtual Screening (SBVS) technique which uses AutoDock Vina - freely available and widely used protein-ligand docking tool. This pipeline has R scripts to perform VS automatically in step-wise manner. To increase the efficiency of VS, we have used data level parallel processing approach using task-pull methodology of Master-Slave communication protocol.

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.