Výsledky vyhledávání - "VANGUNSTEREN, WF"

MOLECULAR-DYNAMICS SIMULATIONS OF OXIDIZED AND REDUCED CLOSTRIDIUM-BEIJERINCKII FLAVODOXIN

Autor: LEENDERS, R, VANGUNSTEREN, WF, BERENDSEN, HJC, VISSER, AJWG

Publikováno v: Biophysical Journal, 66(3), 634-645. CELL PRESS

Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin in water have been performed in a sphere of 1.4-nm radius surrounded by a restrained shell of 0.8 nm. The flavin binding site, comprising the active site of th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=narcis______::90a5b723491606ba63110188880257d3
https://research.rug.nl/en/publications/c72dbcba-ce16-492c-9c54-dc956f398f10

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INFLUENCE OF SOLVENT ON INTRAMOLECULAR PROTON-TRANSFER IN HYDROGEN MALONATE - MOLECULAR-DYNAMICS SIMULATION STUDY OF TUNNELING BY DENSITY-MATRIX EVOLUTION AND NONEQUILIBRIUM SOLVATION

Autor: MAVRI, J, BERENDSEN, HJC, VANGUNSTEREN, WF

Publikováno v: Journal of Physical Chemistry, 97(51), 13469-13476. AMER CHEMICAL SOC

A density matrix evolution (DME) method (Berendsen, H. J. C.; Mavri, J. J. Phys. Chem. the preceding paper in this issue) in combination with classical molecular dynamics simulation was applied to calculate the rate of proton tunneling in the intramo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=narcis______::a244630c6b412fe14896f860e76b0817
https://research.rug.nl/en/publications/2e409d23-c964-4d66-ad94-f1154fc8b0e2

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STRUCTURE PREDICTION OF SUBTILISIN BPN' MUTANTS USING MOLECULAR-DYNAMICS METHODS

Autor: HEINER, AP, BERENDSEN, HJC, VANGUNSTEREN, WF

Publikováno v: Protein Engineering, 6(4), 397-408

In this paper we describe the achievements and pitfalls encountered in doing structure predictions of protein mutants using molecular dynamics simulation techniques in which properties of atoms are slowly changed as a function of time. Basically the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=narcis______::5341be4745e6a6fa3bf1c987217c4c65
https://research.rug.nl/en/publications/aa896841-bd20-4536-8a05-009332efa2b6

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CAN THE STABILITY OF PROTEIN MUTANTS BE PREDICTED BY FREE-ENERGY CALCULATIONS

Autor: Yunyu, S., Alan Mark, Wang, Cx, Huang, Fh, Berendsen, Hjc, Vangunsteren, Wf

Publikováno v: Protein Engineering, 6(3), 289-295
ResearcherID

The use of free energy simulation techniques in the study of protein stability is critically evaluated. Results from two simulations of the thermostability mutation Asn218 to Ser218 in Subtilisin are presented. It is shown that components of the free

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::ed869a009cc09b1533aedd6c5d2c02ec
https://research.rug.nl/en/publications/acb9069d-40d7-4d9a-86d2-466f232b8edb

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CONFORMATIONAL FLEXIBILITY OF AQUEOUS MONOMERIC AND DIMERIC INSULIN - A MOLECULAR-DYNAMICS STUDY

Autor: MARK, AE, BERENDSEN, HJC, VANGUNSTEREN, WF

Publikováno v: Biochemistry, 30(45), 10866-10872. AMER CHEMICAL SOC

A series of molecular dynamics simulations have been used to investigate the nature of monomeric and dimeric insulin in aqueous solution. It is shown that in the absence of crystal contacts both monomeric and dimeric insulin have a high degree of int

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=narcis______::6b6e6a49729e053c1cd86aadfe365937
https://research.rug.nl/en/publications/dd71d776-d9e1-4170-866f-7cf5f4d5dea0

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THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION

Autor: TORDA, AE, VANGUNSTEREN, WF

Publikováno v: Computer Physics Communications, 62(2-3), 289-296. ELSEVIER SCIENCE BV

We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various appro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=narcis______::d36e9d4f3e289062754e05fd298316d4
https://research.rug.nl/en/publications/6d70104a-f9a1-452c-a21b-33431de680af

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ON DERIVING SPATIAL PROTEIN-STRUCTURE FROM NMR OR X-RAY-DIFFRACTION DATA

Autor: Vangunsteren, Wf, Piet Gros, Torda, Ae, Berendsen, Hjc, Vanschaik, Rc

Publikováno v: Ciba foundation symposia, 161, 150-166
Publons

During the last decade it has become possible to derive the spatial structure of small proteins in solution using multidimensional NMR spectroscopy measurements and interpreting the data in terms of a chemical atomic model. The NMR experiments genera

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::e81cadfb254a3d4c9ca7eb093130bdfa
https://research.rug.nl/en/publications/d7412441-e66d-40fd-bc58-e69a9819397b

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