Four X-ray crystallographic structures of the tubulin domain with a high resolution were obtained from the Protein Data Bank (PDB) database (Table 1 ). These structures were firstly preprocessed and used for the generation of pharmacophore models. Hydrogen was added, Gasteiger partial charges were computed, and then energy minimization was carried out using the Merck molecular force field 94× (MMFF94×) forcefield [30 (link)]. Based on these preprocessed crystal structures, the pharmacophore generation protocol of the Molecular Operating Environment (MOE) (Chemical Computing Group Inc., Montreal, Quebec, Canada) was applied to generate the most representative features of the tubulin active site, which are indicated as spheres that represent the essential interaction points with key residues on the ligand binding of the tubulin.
Mmff94 forcefield
Manufactured by Merck Group
The MMFF94× forcefield is a molecular mechanics force field designed for the calculation of molecular structures, energies, and other properties. It is an extension of the MMFF94 force field, which is widely used in the field of computational chemistry. The MMFF94× forcefield provides additional functionality and improvements over the original MMFF94 version.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using mmff94 forcefield
1
Tubulin Pharmacophore Modeling from X-ray Structures
2
Phytochemical Profiling of Patrinia grandiflora
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The information on thirty-four phytochemicals of P. grandiflorus was obtained through a literature search (Zhang et al., 2015 (link)). The structures of the phytochemicals along with Nafamostat (control) were retrieved from the PubChem database (Kim et al., 2016 (link)) and their structures were optimised using Merck molecular force field (MMFF)94 force field (Halgren, 1996 (link)).
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