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A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues Automated webserver and some downloadable programs RaptorX: remote homology detection, protein 3D modeling, binding site prediction
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.
Lead Finder is a computational chemistry tool designed for modelling protein-ligand interactions. It is used for conducting molecular docking studies and quantitatively assessing ligand binding and biological activity. It offers free access to users in commercial, academic, or other settings.
I-TASSER: A standalone I-TASSER package for protein 3D structure prediction and refinement. COACH: A function annotation program based on COFACTOR, TM-SITE and S-SITE. COFACTOR: A program for ligand-binding site, EC number & GO term prediction. TM-SITE: A structure-based approach for ligand-binding site prediction.
University of Washington and The Baker Labs; structure prediction, protein folding Proprietary, commercial or gratis fold.it download page Archived 2011-04-04 at the Wayback Machine: FoldX: I Yes Yes No No No No No No Energy calculations, protein design Proprietary, commercial or gratis CRG: GROMACS: No No Yes Yes No [2] Yes I Yes [3] Yes High ...
The goal of protein–ligand docking is to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme. [1] Pharmaceutical research employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals in order to select ...
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.
CAMEO performs blind assessment of protein structure prediction techniques based on the weekly releases of newly determined experimental structures by the Protein Databank (PDB). The amino acid sequences of soon to be released protein structures are submitted to the participating web-servers. The web-servers return their predictions to CAMEO ...
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