In Silico 3D Modeling of Binding Activities.
In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available.
Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy. stefano.moro@unipd.it.
Stefano
S
Moro
Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy.
Mattia
M
Sturlese
Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy.
Antonella
A
Ciancetta
Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, v.le San Pietro 43/C, 07100, Sassari, Italy.
Matteo
M
Floris
D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008024:Ligands; D008958:Models, Molecular; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D021281:Quantitative Structure-Activity Relationship
D008024:Ligands; D011506:Proteins
Binding affinity prediction; Chemical risk assessment; Molecular docking; Molecular modeling; Scoring function