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Publication for LigandScout
How Diverse Are the Protein Bound Conformations of Small Molecule Drugs and Cofactors?
[…] aestro (Schrödinger Release 2016-2: Maestro, Schrödinger, LLC, New York, NY, 2016), MOE (Molecular Operating Environment (MOE), version 2016.08; Chemical Computing Group Inc.: Montreal, QC, 2016) and LigandScout (LigandScout, version 4.2; Inte:Ligand GmbH: Vienna, Austria, 2017; Wolber and Langer, ), respectively.For the sake of clarity, all hydrogens, only polar hydrogens or no hydrogens were inc […]
Computer Aided Drug Design in Epigenetics
[…] r compound collection, the ChemBridge database containing 328,000 molecules (Heinke et al., ). Based on previously reported binding modes of allantodapsone, the pharmacophore models were generated in LigandScout with one HBD, one hydrogen bond acceptor (HBA), two hydrophobic/aromatic features, one included volume and 23 excluded volumes leading to the identification of nine compounds with PRMT1 in […]
Pharmacophore Modeling and in Silico/in Vitro Screening for Human Cytochrome P450 11B1 and Cytochrome P450 11B2 Inhibitors
[…] After removing duplicates, 15948 decoys remained in the database. The 2D structures of all active compounds were constructed in ChemBioDraw Ultra 14.0 (Cambridgesoft, ). For conformational analysis, LigandScout 3.12 (Wolber and Langer, ) generated up to 500 conformers for each compound in the dataset with OMEGA-BEST (Hawkins et al., ; Hawkins and Nicholls, ) settings. […]
An Integrated Computational Approach for Plant Based Protein Tyrosine Phosphatase Non Receptor Type 1 Inhibitors
[…] Eleven compounds were used as a training set based on their physiochemical properties, Lipinski’s filter, and IC50 values less than 10μM. These 11 compounds were used for pharmacophore modeling using LigandScout 4.1 . ChemDraw Ultra 8.0 software  is used for sketching chemical structure of training dataset and saved in Protein Data Bank (PDB) format. Consequently, these files were used as inpu […]
Pyridoxine dipharmacophore derivatives as potent glucokinase activators for the treatment of type 2 diabetes mellitus
[…] s data, using the PyRx 0.8 program https://sourceforge.net/projects/pyrx/, where the docking space covering the allosteric GK site was built. Analysis of the binding mechanism was performed using the LigandScout 4.1 program (Ligand GmbH. http://www.inteligand.com/ligandscout/). […]
Targeting Dengue Virus NS 3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening
[…] All the computation experiments were performed on Windows 8 workstation. LigandScout version 3.12 (Wolber and Langer, ) was used for pharmacophore modeling. The X-ray crystallography structure of DENV-2 NS-3 helicase [PDB ID: 2BMF (Xu et al., )] was retrieved from RCSB Pro […]
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