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Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations
KTH, School of Chemical Science and Engineering (CHE).
2015 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Bindningsenergier för komplex mellan ligander och proteiner beräknade med molekyldynamiksimuleringar (Swedish)
Abstract [en]

Indications that existing parameter sets of extended Linear Interaction Energy (LIE) models are transferable between lipases from Rhizomucor Miehei and Thermomyces Lanigunosus in complex with a small set of vinyl esters are demonstrated. By calculat- ing energy terms that represents the cost of forming cavities filled by the ligand and the complex we can add them to a LIE model with en established parameter set. The levels of precision attained will be comparable to those of an optimal fit. It is also demonstrated that the Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods are in- applicable to the problem of calculating absolute binding energies, even when the largest source of variance has been reduced.

Place, publisher, year, edition, pages
2015. , 30 p.
Keyword [en]
Molecular Dynamics, Linear Interaction Energy, Enzyme Design, Lipase, Binding Energy
National Category
Engineering and Technology
URN: urn:nbn:se:kth:diva-170722OAI: diva2:839581
Available from: 2015-07-03 Created: 2015-07-03 Last updated: 2015-07-03Bibliographically approved

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