Dynameomics

A Comprehensive Database of Protein Dynamics

Marc W. van der Kamp, R. Dustin Schaeffer, Amanda L. Jonsson, Alexander D. Scouras, Andrew M. Simms, Rudesh D. Toofanny, Noah C. Benson, Peter C. Anderson, Eric D. Merkley, Steven Rysavy, Dennis Bromley, David A.C. Beck, Valerie Daggett

Research output: Contribution to journalArticle

93 Citations (Scopus)

Abstract

The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (∼11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.

Original languageEnglish (US)
Pages (from-to)423-435
Number of pages13
JournalStructure
Volume18
Issue number4
DOIs
StatePublished - Mar 1 2010

Fingerprint

Protein Databases
Protein Folding
Databases
Proteins
Protein Unfolding
Drug Design
Molecular Dynamics Simulation
Single Nucleotide Polymorphism
Peptides

Keywords

  • Proteins

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

van der Kamp, M. W., Schaeffer, R. D., Jonsson, A. L., Scouras, A. D., Simms, A. M., Toofanny, R. D., ... Daggett, V. (2010). Dynameomics: A Comprehensive Database of Protein Dynamics. Structure, 18(4), 423-435. https://doi.org/10.1016/j.str.2010.01.012

Dynameomics : A Comprehensive Database of Protein Dynamics. / van der Kamp, Marc W.; Schaeffer, R. Dustin; Jonsson, Amanda L.; Scouras, Alexander D.; Simms, Andrew M.; Toofanny, Rudesh D.; Benson, Noah C.; Anderson, Peter C.; Merkley, Eric D.; Rysavy, Steven; Bromley, Dennis; Beck, David A.C.; Daggett, Valerie.

In: Structure, Vol. 18, No. 4, 01.03.2010, p. 423-435.

Research output: Contribution to journalArticle

van der Kamp, MW, Schaeffer, RD, Jonsson, AL, Scouras, AD, Simms, AM, Toofanny, RD, Benson, NC, Anderson, PC, Merkley, ED, Rysavy, S, Bromley, D, Beck, DAC & Daggett, V 2010, 'Dynameomics: A Comprehensive Database of Protein Dynamics', Structure, vol. 18, no. 4, pp. 423-435. https://doi.org/10.1016/j.str.2010.01.012
van der Kamp MW, Schaeffer RD, Jonsson AL, Scouras AD, Simms AM, Toofanny RD et al. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure. 2010 Mar 1;18(4):423-435. https://doi.org/10.1016/j.str.2010.01.012
van der Kamp, Marc W. ; Schaeffer, R. Dustin ; Jonsson, Amanda L. ; Scouras, Alexander D. ; Simms, Andrew M. ; Toofanny, Rudesh D. ; Benson, Noah C. ; Anderson, Peter C. ; Merkley, Eric D. ; Rysavy, Steven ; Bromley, Dennis ; Beck, David A.C. ; Daggett, Valerie. / Dynameomics : A Comprehensive Database of Protein Dynamics. In: Structure. 2010 ; Vol. 18, No. 4. pp. 423-435.
@article{39a52c52e8c2469e801fde054d83bbf3,
title = "Dynameomics: A Comprehensive Database of Protein Dynamics",
abstract = "The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (∼11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.",
keywords = "Proteins",
author = "{van der Kamp}, {Marc W.} and Schaeffer, {R. Dustin} and Jonsson, {Amanda L.} and Scouras, {Alexander D.} and Simms, {Andrew M.} and Toofanny, {Rudesh D.} and Benson, {Noah C.} and Anderson, {Peter C.} and Merkley, {Eric D.} and Steven Rysavy and Dennis Bromley and Beck, {David A.C.} and Valerie Daggett",
year = "2010",
month = "3",
day = "1",
doi = "10.1016/j.str.2010.01.012",
language = "English (US)",
volume = "18",
pages = "423--435",
journal = "Structure with Folding & design",
issn = "0969-2126",
publisher = "Cell Press",
number = "4",

}

TY - JOUR

T1 - Dynameomics

T2 - A Comprehensive Database of Protein Dynamics

AU - van der Kamp, Marc W.

AU - Schaeffer, R. Dustin

AU - Jonsson, Amanda L.

AU - Scouras, Alexander D.

AU - Simms, Andrew M.

AU - Toofanny, Rudesh D.

AU - Benson, Noah C.

AU - Anderson, Peter C.

AU - Merkley, Eric D.

AU - Rysavy, Steven

AU - Bromley, Dennis

AU - Beck, David A.C.

AU - Daggett, Valerie

PY - 2010/3/1

Y1 - 2010/3/1

N2 - The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (∼11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.

AB - The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (∼11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.

KW - Proteins

UR - http://www.scopus.com/inward/record.url?scp=77951680969&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77951680969&partnerID=8YFLogxK

U2 - 10.1016/j.str.2010.01.012

DO - 10.1016/j.str.2010.01.012

M3 - Article

VL - 18

SP - 423

EP - 435

JO - Structure with Folding & design

JF - Structure with Folding & design

SN - 0969-2126

IS - 4

ER -