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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.
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 only required input is a protein sequence for the prediction of the protein 3D structure and function. [1] The IntFOLD output is presented via a user-friendly interface for the use of life scientists. The raw data is also formatted in Critical Assessment of Methods for Protein Structure Prediction (CASP) standards with a detailed help page. [1]
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.
Following a molecular docking stage that generates potential ligand conformations, a scoring stage assesses the interaction strength between each ligand's pose and the protein. [4] The pipeline ultimately produces a ranking of hit compounds as its output, indicating the most promising candidates for further investigation.
POAP is a shell-script-based tool which automates AutoDock for virtual screening from ligand preparation to post docking analysis. [ 26 ] VirtualFlow allows to carry out ultra-large virtual screenings on computer clusters and the cloud using AutoDock Vina-based docking programs, allowing to routinely screen billions of compounds.
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.
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 ...