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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
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.
ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure. Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dušanka Janežič in 2010 [1] and is now available as ProBiS server, ProBiS CHARMMing server, ProBiS algorithm and ProBiS plugin.
TM-SITE: A structure-based approach for ligand-binding site prediction. S-SITE: A sequence-based approach for ligand-binding site prediction. LOMETS: A set of locally installed threading programs for meta-server protein fold-recognition. MUSTER: A threading program to identify templates from a non-redundant protein structure library.
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.
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 ...
A protein-ligand binding challenge on PHIPA fragments was also included. Host-guest binding focused on several small molecules binding to octa-acid and exo-octa-acid; binding of two compounds to a series of cyclodextrin derivatives; and binding of a series of small molecules to a clip-like guest known as TrimerTrip.
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.