Biomolecular modeling: Goals, problems, perspectives

Wilfred F. Van Gunsteren; Dirk Bakowies; Riccardo Baron; Indira Chandrasekhar; Markus Christen; Xavier Daura; Peter Gee; Daan P. Geerke; Alice Glättli; Philippe H. Hünenberger; Mika A. Kastenholz; Chris Oostenbrink; Merijn Schenk; Daniel Trzesniak; Nico F.A. Van Der Vegt; Haibo B. Yu

doi:10.1002/anie.200502655

Biomolecular modeling: Goals, problems, perspectives

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

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Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.

Idioma original	Anglès
Pàgines (de-a)	4064-4092
Revista	Angewandte Chemie - International Edition
Volum	45
Número	25
DOIs	https://doi.org/10.1002/anie.200502655
Estat de la publicació	Publicada - 19 de juny 2006

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10.1002/anie.200502655

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Van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., Kastenholz, M. A., Oostenbrink, C., Schenk, M., Trzesniak, D., Van Der Vegt, N. F. A., & Yu, H. B. (2006). Biomolecular modeling: Goals, problems, perspectives. Angewandte Chemie - International Edition, 45(25), 4064-4092. https://doi.org/10.1002/anie.200502655

@article{56b8563fb1004b11b6166e2e617187f1,

title = "Biomolecular modeling: Goals, problems, perspectives",

abstract = "Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling. {\textcopyright} 2006 Wiley-VCH Verlag GmbH & Co. KGaA.",

keywords = "Computer simulation, Force-field techniques, GROMOS, Molecular dynamics, Molecular modeling",

author = "{Van Gunsteren}, {Wilfred F.} and Dirk Bakowies and Riccardo Baron and Indira Chandrasekhar and Markus Christen and Xavier Daura and Peter Gee and Geerke, {Daan P.} and Alice Gl{\"a}ttli and H{\"u}nenberger, {Philippe H.} and Kastenholz, {Mika A.} and Chris Oostenbrink and Merijn Schenk and Daniel Trzesniak and {Van Der Vegt}, {Nico F.A.} and Yu, {Haibo B.}",

year = "2006",

month = jun,

day = "19",

doi = "10.1002/anie.200502655",

language = "English",

volume = "45",

pages = "4064--4092",

journal = "Angewandte Chemie - International Edition",

issn = "1433-7851",

publisher = "John Wiley and Sons Ltd",

number = "25",

}

Van Gunsteren, WF, Bakowies, D, Baron, R, Chandrasekhar, I, Christen, M, Daura, X, Gee, P, Geerke, DP, Glättli, A, Hünenberger, PH, Kastenholz, MA, Oostenbrink, C, Schenk, M, Trzesniak, D, Van Der Vegt, NFA & Yu, HB 2006, 'Biomolecular modeling: Goals, problems, perspectives', Angewandte Chemie - International Edition, vol. 45, núm. 25, pàg. 4064-4092. https://doi.org/10.1002/anie.200502655

TY - JOUR

T1 - Biomolecular modeling: Goals, problems, perspectives

AU - Van Gunsteren, Wilfred F.

AU - Bakowies, Dirk

AU - Baron, Riccardo

AU - Chandrasekhar, Indira

AU - Christen, Markus

AU - Daura, Xavier

AU - Gee, Peter

AU - Geerke, Daan P.

AU - Glättli, Alice

AU - Hünenberger, Philippe H.

AU - Kastenholz, Mika A.

AU - Oostenbrink, Chris

AU - Schenk, Merijn

AU - Trzesniak, Daniel

AU - Van Der Vegt, Nico F.A.

AU - Yu, Haibo B.

PY - 2006/6/19

Y1 - 2006/6/19

N2 - Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.

AB - Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.

KW - Computer simulation

KW - Force-field techniques

KW - GROMOS

KW - Molecular dynamics

KW - Molecular modeling

U2 - 10.1002/anie.200502655

DO - 10.1002/anie.200502655

M3 - Review article

SN - 1433-7851

VL - 45

SP - 4064

EP - 4092

JO - Angewandte Chemie - International Edition

JF - Angewandte Chemie - International Edition

IS - 25

ER -

Biomolecular modeling: Goals, problems, perspectives

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