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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 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.
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.
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.
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 ...
New experimental data, such as binding affinity and hydration free energy, are withheld from participants until the prediction submission deadline, so that the true predictive power of methods can be revealed. The most recent SAMPL5 challenge contains two prediction categories: the binding affinity of host–guest systems, and the distribution ...
(I) Free energy perturbation (FEP) simulations, (II) empirical valence bond (EVB), calculations of reaction free energies, (III) linear interaction energy (LIE) calculations of receptor-ligand binding affinities Free open source GNU GPLv2 or later Q: QuantumATK: Yes Yes Yes Yes Yes No Yes Yes Yes Complete atomistic modeling platform for ...