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2017 ; 9
(2
): 91-102
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Software for molecular docking: a review
#MMPMID28510083
Pagadala NS
; Syed K
; Tuszynski J
Biophys Rev
2017[Apr]; 9
(2
): 91-102
PMID28510083
show ga
Molecular docking methodology explores the behavior of small molecules in the
binding site of a target protein. As more protein structures are determined
experimentally using X-ray crystallography or nuclear magnetic resonance (NMR)
spectroscopy, molecular docking is increasingly used as a tool in drug discovery.
Docking against homology-modeled targets also becomes possible for proteins whose
structures are not known. With the docking strategies, the druggability of the
compounds and their specificity against a particular target can be calculated for
further lead optimization processes. Molecular docking programs perform a search
algorithm in which the conformation of the ligand is evaluated recursively until
the convergence to the minimum energy is reached. Finally, an affinity scoring
function, ?G [U total in kcal/mol], is employed to rank the candidate poses as
the sum of the electrostatic and van der Waals energies. The driving forces for
these specific interactions in biological systems aim toward complementarities
between the shape and electrostatics of the binding site surfaces and the ligand
or substrate.
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