Výsledky vyhledávání - "Daniel Trzesniak"

Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models

Autor: Riccardo Baron, Daniel Trzesniak, Andreas Elsener, Alex H. de Vries, Siewert J. Marrink, Wilfred F. van Gunsteren

Publikováno v: Chemphyschem, 8(3), 452-461. WILEY-V C H VERLAG GMBH

Thermodynamic data are often used to calibrate or test atomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e1585db11aca43b73c46e649b4f0137
https://doi.org/10.1002/cphc.200600658

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A Comparison of Methods to Compute the Potential of Mean Force

Autor: Anna-Pitschna E. Kunz, Daniel Trzesniak, Wilfred F. van Gunsteren

Publikováno v: ChemPhysChem. 8:162-169

Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected b

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8957a60075307cd95ff44d1a4ec61869
https://doi.org/10.1002/cphc.200600527

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Analysis of neo-pentane–urea pair potentials of mean force in aqueous urea

Autor: N.F.A. van der Vegt, Daniel Trzesniak, W. F. van Gunsteren

Publikováno v: Molecular Physics. 105:33-39

Urea is often used as a denaturant in protein (un)folding studies because it alters the way hydrophobic solutes and water affect one another. The solvation structure of neo-pentane and urea in 6.9 M urea aqueous solution are investigated by analysing

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::cbba5b6f52a5a36163e3279512bc6b34
https://doi.org/10.1080/00268970601126742

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Modelagem quântica de inibidores enzimáticos

Autor: Daniel Trzesniak

Publikováno v: Biblioteca Digital de Teses e Dissertações da USP
Universidade de São Paulo (USP)
instacron:USP

Realizamos uma caracterização estrutural e eletrônica dos inibidores enzimáticos E-64 e CA030 utilizando técnicas de química quântica. Otimizações de geometria são realizadas em nível ab initio com os métodos Hartree-Fock e Teoria do Func

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6917f303faa614cd8b33bd9f47eb48da
https://doi.org/10.11606/d.43.2002.tde-26062002-143722

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Pathway dependence of the efficiency of calculating free energy and entropy of solute–solute association in water

Autor: Daniel Trzesniak, Wilfred F. van Gunsteren

Publikováno v: Chemical Physics. 330:410-416

In this study we investigate two alternative pathways to compute the free energy and the entropy of small molecule association (Δ F assoc and Δ S assoc ) in water. The first route (direct pathway) uses thermodynamic integration as function of the d

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ede8ce6b9879db6f728e5ac6d6538ba9
https://doi.org/10.1016/j.chemphys.2006.09.012

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Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: Pathway prediction and reconciliation of X-ray crystallographic and NMR solution data

Autor: Wilfred F. van Gunsteren, Daniel Trzesniak

Publikováno v: Protein Science. 15:2544-2551

Cyclophilins are proteins that catalyze X-proline cis–trans interconversion, where X represents any amino acid. Its mechanism of action has been investigated over the past years but still generates discussion, especially because until recently stru

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b17a4da32413e415d35cc7fe49834030
https://doi.org/10.1110/ps.062356406

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Protein under pressure: Molecular dynamics simulation of the arc repressor

Autor: Roberto D. Lins, Daniel Trzesniak, Wilfred F. van Gunsteren

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 65:136-144

Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen-bonding pattern of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::309fc6e0b0031dd818ae4a0314d412a7
https://doi.org/10.1002/prot.21034

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Biomolekulare Modellierung: Ziele, Probleme, Perspektiven

Autor: Merijn Schenk, Daniel Trzesniak, Xavier Daura, Mika A. Kastenholz, Chris Oostenbrink, Riccardo Baron, Markus Christen, Indira Chandrasekhar, Nico F. A. van der Vegt, Peter J. Gee, Alice Glättli, Philippe H. Hünenberger, Dirk Bakowies, Haibo Yu, Daan P. Geerke, Wilfred F. van Gunsteren

Publikováno v: Angewandte Chemie. 118:4168-4198

Computerverfahren auf der Grundlage von Molekulmodellen gewinnen in Biologie, biologischer Chemie und Biophysik zunehmend an Bedeutung. Da nur wenige Eigenschaften biomolekularer Systeme durch Messungen zuganglich sind, konnen Computersimulationen ex

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https://doi.org/10.1002/ange.200502655

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Interpreting NMR Data for β-Peptides Using Molecular Dynamics Simulations

Autor: Wilfred F. van Gunsteren, Alice Glättli, Daniel Trzesniak, Bernhard Jaun

Publikováno v: Journal of the American Chemical Society. 127:14320-14329

NMR is one of the most used techniques to resolve structure of proteins and peptides in solution. However, inconsistencies may occur due to the fact that a polypeptide may adopt more than one conformation. Since the NOE distance bounds and (3)J-value

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::068f7bcedd3679dea5e99a8340ed8dbd
https://doi.org/10.1021/ja044285h

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The GROMOS software for biomolecular simulation: GROMOS05

Autor: Dirk Bakowies, Daniel Trzesniak, Philippe H. Hünenberger, Chris Oostenbrink, Mika A. Kastenholz, Riccardo Baron, Markus Christen, Christine Peter, Vincent Kräutler, Daan P. Geerke, Wilfred F. van Gunsteren, Tim N. Heinz, Roland Bürgi

Publikováno v: Christen, M, Hunenberger, P H, Bakowies, D, Baron, R, Burgi, R, Geerke, D P, Heinz, T N, Kastenholz, M, Krautler, V, Oostenbrink, C, Peter, C, Trzesniak, D & van Gunsteren, W F 2005, ' The GROMOS software for biomolecular simulation: GROMOS05 ', Journal of Computational Chemistry, vol. 26, no. 16, pp. 1719-51 . https://doi.org/10.1002/jcc.20303
Journal of Computational Chemistry, 26(16), 1719-51. John Wiley and Sons Inc.

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f771c6fbfcfcecaf3f5bca54ecad342
https://doi.org/10.1002/jcc.20303

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