Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations
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)
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.
Molecular Dynamics, Linear Interaction Energy, Enzyme Design, Lipase, Binding Energy
Engineering and Technology
IdentifiersURN: urn:nbn:se:kth:diva-170722OAI: oai:DiVA.org:kth-170722DiVA: diva2:839581