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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.
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]
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 ...
rDock (previously RiboDock) is an open-source molecular docking software that be used for docking small molecules against proteins and nucleic acids. It is primarily designed for high-throughput virtual screening and prediction of binding mode.
Molecular docking research focuses on computationally simulating the molecular recognition process. It aims to achieve an optimized conformation for both the protein and ligand and relative orientation between protein and ligand such that the free energy of the overall system is minimized.
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 ...
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.
Glide is a molecular modeling software for docking of small molecules into proteins and other biopolymers. [1] [2] It was developed by Schrödinger, Inc. References