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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.
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
Computer program for general purpose molecular modelling for molecular design and simulations. Windows: GPLv2: Agile Molecule AutoDock: Suite of automated docking tools Linux, Mac OS X, SGI IRIX, and Windows: GPL: Scripps Research: Avogadro
Small molecule docking to nucleic acids with water placement: ... Comparison of software for molecular mechanics modeling; List of software for Monte Carlo molecular ...
List of gene prediction software; List of disorder prediction software; List of Protein subcellular localization prediction tools; List of phylogenetics software; List of phylogenetic tree visualization software; Category:Metagenomics_software; Structural biology software. List of molecular graphics systems; List of protein-ligand docking ...
This is a list of notable software systems that are used for visualizing macromolecules. ... structure prediction and docking. Graphical or text mode (clusters ...
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry , such software directly supports the aspects related to constructing molecular models, including:
Several protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide. Peptides are a highly flexible type of ligand that has proven to be a ...
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