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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.
Java library functions for manipulating sequences, protein structures, file parsers, CORBA interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines Linux, macOS, Windows: LGPL v2.1 Open Bioinformatics Foundation: BioJS: JavaScript library of components to visualize biological data
Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. Proprietary, trial available
AutoDock runs on Linux, Mac OS X, SGI IRIX, and Microsoft Windows. [11] It is available as a package in several Linux distributions, including Debian, [12] [13] Fedora, [14] and Arch Linux. [15] Compiling the application in native 64-bit mode on Microsoft Windows enables faster floating-point operation of the software. [16]
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Spectrolyzer is a Microsoft Windows-based software package developed by Binary Detect (previously named Medicwave) that provides bioinformatics data analysis tools for different mass spectrometers. It focuses on finding protein biomarkers and detecting protein deviations. Spectromania Proprietary
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