Biomolecular modeling and simulation: A field coming of age

Tamar Schlick, Rosana Collepardo-Guevara, Leif Arthur Halvorsen, Segun Jung, Xia Xiao

Research output: Contribution to journalArticle

Abstract

We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field's history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.

Original languageEnglish (US)
Pages (from-to)191-228
Number of pages38
JournalQuarterly Reviews of Biophysics
Volume44
Issue number2
DOIs
StatePublished - May 2011

Fingerprint

Protein Folding
History
RNA
Ligands
Technology
Proteins

ASJC Scopus subject areas

  • Biophysics

Cite this

Biomolecular modeling and simulation : A field coming of age. / Schlick, Tamar; Collepardo-Guevara, Rosana; Halvorsen, Leif Arthur; Jung, Segun; Xiao, Xia.

In: Quarterly Reviews of Biophysics, Vol. 44, No. 2, 05.2011, p. 191-228.

Research output: Contribution to journalArticle

Schlick, T, Collepardo-Guevara, R, Halvorsen, LA, Jung, S & Xiao, X 2011, 'Biomolecular modeling and simulation: A field coming of age', Quarterly Reviews of Biophysics, vol. 44, no. 2, pp. 191-228. https://doi.org/10.1017/S0033583510000284
Schlick, Tamar ; Collepardo-Guevara, Rosana ; Halvorsen, Leif Arthur ; Jung, Segun ; Xiao, Xia. / Biomolecular modeling and simulation : A field coming of age. In: Quarterly Reviews of Biophysics. 2011 ; Vol. 44, No. 2. pp. 191-228.
@article{79c160992ed54b1188b232c113d3ff44,
title = "Biomolecular modeling and simulation: A field coming of age",
abstract = "We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field's history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.",
author = "Tamar Schlick and Rosana Collepardo-Guevara and Halvorsen, {Leif Arthur} and Segun Jung and Xia Xiao",
year = "2011",
month = "5",
doi = "10.1017/S0033583510000284",
language = "English (US)",
volume = "44",
pages = "191--228",
journal = "Quarterly Reviews of Biophysics",
issn = "0033-5835",
publisher = "Cambridge University Press",
number = "2",

}

TY - JOUR

T1 - Biomolecular modeling and simulation

T2 - A field coming of age

AU - Schlick, Tamar

AU - Collepardo-Guevara, Rosana

AU - Halvorsen, Leif Arthur

AU - Jung, Segun

AU - Xiao, Xia

PY - 2011/5

Y1 - 2011/5

N2 - We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field's history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.

AB - We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field's history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.

UR - http://www.scopus.com/inward/record.url?scp=79956058665&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79956058665&partnerID=8YFLogxK

U2 - 10.1017/S0033583510000284

DO - 10.1017/S0033583510000284

M3 - Article

C2 - 21226976

AN - SCOPUS:79956058665

VL - 44

SP - 191

EP - 228

JO - Quarterly Reviews of Biophysics

JF - Quarterly Reviews of Biophysics

SN - 0033-5835

IS - 2

ER -