Browsing by Author "Karplus, M."
Now showing items 1-9 of 9
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Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
Archontis, Georgios Z.; Simonson, T.; Karplus, M. (2001)Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to ...
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CHARMM: The biomolecular simulation program
Brooks, B. R.; Brooks III, C. L.; Mackerell Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, Georgios Z.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009)CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, ...
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Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
Simonson, T.; Archontis, Georgios Z.; Karplus, M. (1997)A method is proposed to include long-range electrostatic interactions in free energy calculations that involve the creation or deletion of net charges in a macromolecule. The vicinity of the mutation site is treated ...
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Cumulant expansion of the free energy: Application to free energy derivatives and component analysis
Archontis, Georgios Z.; Karplus, M. (1996)The free-energy change in a system represented by an empirical energy function, when calculated by thermodynamic integration from the initial to the final state, can be expressed as a sum of "free-energy components," that ...
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Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics
Lazaridis, T.; Archontis, Georgios Z.; Karplus, M. (1995)This chapter discusses published analyses of protein stability based on model compound data and outlines the assumptions that have been made. The enthalpy of protein folding is considered and a thermodynamic cycle is used ...
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Free energy simulations come of age: Protein-ligand recognition
Simonson, T.; Archontis, Georgios Z.; Karplus, M. (2002)In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide ...
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Free energy simulations: The meaning of the individual contributions from a component analysis
Boresch, S.; Archontis, Georgios Z.; Karplus, M. (1994)A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred ...
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Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues
Archontis, Georgios Z.; Watson, K. A.; Xie, Q.; Andreou, Georgia; Chrysina, Evangelia D.; Zographos, Spyros E.; Oikonomakos, Nikos G.; Karplus, M. (2005)GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could ...
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Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
Archontis, Georgios Z.; Simonson, T.; Moras, D.; Karplus, M. (1998)Specific amino acid binding by aminoacyl-tRNA synthetases is necessary for correct translation of the genetic code. To obtain insight into the origin of the specificity, the binding to aspartyl-tRNA synthetase (AspRS) of ...