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  2. List of protein-ligand docking software - Wikipedia

    en.wikipedia.org/wiki/List_of_protein-ligand...

    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.

  3. rDock - Wikipedia

    en.wikipedia.org/wiki/RDock

    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.

  4. List of open-source bioinformatics software - Wikipedia

    en.wikipedia.org/wiki/List_of_open-source...

    Apache Software Foundation, myGrid: Ascalaph Designer: 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

  5. Comparison of software for molecular mechanics modeling

    en.wikipedia.org/wiki/Comparison_of_software_for...

    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 ...

  6. LeDock - Wikipedia

    en.wikipedia.org/wiki/LeDock

    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.

  7. AutoDock - Wikipedia

    en.wikipedia.org/wiki/AutoDock

    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]

  8. Comparison of nucleic acid simulation software - Wikipedia

    en.wikipedia.org/wiki/Comparison_of_nucleic_acid...

    Small molecule docking to nucleic acids with water placement: Free for academia, Proprietary: Molecular Forecaster Archived ... List of software for Monte Carlo ...

  9. FlexAID - Wikipedia

    en.wikipedia.org/wiki/FlexAID

    FlexAID is a molecular docking software that can use small molecules and peptides as ligands and proteins and nucleic acids as docking targets. As the name suggests, FlexAID supports full ligand flexibility as well side-chain flexibility of the target.