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AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the research community. [1]
The number of notable protein-ligand docking programs currently available is high and has been steadily increasing over the last decades. The following list presents an overview of the most common notable programs, listed alphabetically, with indication of the corresponding year of publication, involved organisation or institution, short description, availability of a webservice and the license.
MOE: Yes Yes Yes Yes No No I Yes No Molecular Operating Environment (MOE) Proprietary: Chemical Computing Group: ms2: Yes Yes Yes Yes Yes No No No No direct on the fly computation of large number of thermophysical properties. Main application of ms2 is on fluids. Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes
LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows. [2] [3] [4] The software can run as a standalone programme or from Jupyter Notebook. [5] It supports the Tripos Mol2 file format.
Software for analysis of 16S rRNA gene amplicon sequence data Linux, macOS, Windows: GPL: University of Michigan: Nextflow: A workflow management system used for building and running scalable and reproducible bioinformatics pipelines, especially in cloud and high-performance computing environments. Linux, macOS, Windows: Apache License 2.0 ...
The Molecular Operating Environment was developed by the Chemical Computing Group under the supervision of President/CEO Paul Labute. [3] Founded in 1994 [ 4 ] and based in Montreal, Quebec, Canada, this private company is dedicated to developing computation software that will challenge, revolutionize, and aid in the scientific methodology.
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UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1] High-quality images and movies can be created.