ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

Jonathan Binkley; Kalpana Karra; Andrew Kirby; Midori Hosobuchi; Eric A. Stone; Arend Sidow

doi:10.1101/gr.097121.109

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

Jonathan Binkley, Kalpana Karra, Andrew Kirby, Midori Hosobuchi, Eric A. Stone, Arend Sidow^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

28 Citations (Scopus)

Abstract

ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The "ProPhylER Interface" displays predictive analyses in sequence space; the "CrystalPainter" maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylER's unique regional analysis of evolutionary constraint. The high accuracy of ProPhylER's regional analysis complements the high resolution of its single-site analysis to effectively guide and inform structure-function investigations and predict the impact of polymorphisms.

Original language	English
Pages (from-to)	142-154
Number of pages	13
Journal	Genome Research
Volume	20
Issue number	1
DOIs	https://doi.org/10.1101/gr.097121.109
Publication status	Published - Jan 2010
Externally published	Yes

Access to Document

10.1101/gr.097121.109

Cite this

@article{28dc8551516943579dddbd8ff3e5f3c8,

title = "ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses",

abstract = "ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The {"}ProPhylER Interface{"} displays predictive analyses in sequence space; the {"}CrystalPainter{"} maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylER's unique regional analysis of evolutionary constraint. The high accuracy of ProPhylER's regional analysis complements the high resolution of its single-site analysis to effectively guide and inform structure-function investigations and predict the impact of polymorphisms.",

author = "Jonathan Binkley and Kalpana Karra and Andrew Kirby and Midori Hosobuchi and Stone, {Eric A.} and Arend Sidow",

year = "2010",

month = jan,

doi = "10.1101/gr.097121.109",

language = "English",

volume = "20",

pages = "142--154",

journal = "Genome Research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

number = "1",

}

TY - JOUR

T1 - ProPhylER

T2 - A curated online resource for protein function and structure based on evolutionary constraint analyses

AU - Binkley, Jonathan

AU - Karra, Kalpana

AU - Kirby, Andrew

AU - Hosobuchi, Midori

AU - Stone, Eric A.

AU - Sidow, Arend

PY - 2010/1

Y1 - 2010/1

N2 - ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The "ProPhylER Interface" displays predictive analyses in sequence space; the "CrystalPainter" maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylER's unique regional analysis of evolutionary constraint. The high accuracy of ProPhylER's regional analysis complements the high resolution of its single-site analysis to effectively guide and inform structure-function investigations and predict the impact of polymorphisms.

AB - ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The "ProPhylER Interface" displays predictive analyses in sequence space; the "CrystalPainter" maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylER's unique regional analysis of evolutionary constraint. The high accuracy of ProPhylER's regional analysis complements the high resolution of its single-site analysis to effectively guide and inform structure-function investigations and predict the impact of polymorphisms.

UR - http://www.scopus.com/inward/record.url?scp=74949129174&partnerID=8YFLogxK

U2 - 10.1101/gr.097121.109

DO - 10.1101/gr.097121.109

M3 - Article

SN - 1088-9051

VL - 20

SP - 142

EP - 154

JO - Genome Research

JF - Genome Research

IS - 1

ER -

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

Abstract

Access to Document

Other files and links

Fingerprint

Cite this