Search Results for "autodock vina"
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Showing 12 open source projects for "autodock vina"
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smina
Scoring and Minimization with AutoDock Vina
A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. -
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AutoDockParser
A tool for efficient processing of Docking results
AutoDock Suit is one of the most popular software for performing Molecular Docking and Virtual Screening. This suit offers two programs AutoDock and AutoDock Vina. AutoDock provides its output as Docking Log Files (DLG files), while the latter outputs in pdbqt format. Post-processing of these results has long remained a manual job and hence various protocols and workflows are designed that are user-specific. -
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
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... -
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Jupyter Dock
Perform molecular docking protocols interactively
...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. -
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GWOVina 1.0
The Hybrid Grey Wolf Optimization for Protein-Ligand Docking
...Its success rate is higher than AutoDock Vina, but similar to AutoDockFR. https://cbbio.online/software/gwovina/index.html -
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PSOVina 2.0
The Hybrid Particle Swarm Optimization for Protein-Ligand Docking
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 -
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AutoDock Vina 1.1.2 - 64-bit
Compilation of AutoDock Vina 1.1.2 for x86_64 system CentOS 6.7.
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. -
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(NCS) NEQUIM Contact System
Tool for analyze of interactions in ligand-protein complexes
...Core features include multiple views of vectors, multiple selection options, cluster analysis and generation of interaction vector model. The input could be from PDB format or from files generated by automatic docking softwares AutoDock/Vina or Surflex. -
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ASM docking portlet
Portlet, interface to submit autodock based molecule docking
Portlet, java web interface to submit distributed autodock/autodock vina based molecule docking. Submit workunits and visualize them. -
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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..
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Autmated Peptide Screening
Screening peptides for MHC and/or MHC-T cell receptor affinity
Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. ... -
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ParallelVSR
ParallelVSR - a pipeline for parallel virtual screening on R platform
...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.
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