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

被引：29

作者：

Binkley, Jonathan ^{[1
,2
]}

Karra, Kalpana ^{[1
,2
]}

Kirby, Andrew

Hosobuchi, Midori ^{[1
,2
]}

Stone, Eric A. ^{[3
,4
]}

Sidow, Arend ^{[1
,2
]}

机构：

[1] Stanford Univ, Dept Pathol, Sch Med, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA

[3] N Carolina State Univ, Dept Stat, Raleigh, NC 27695 USA

[4] N Carolina State Univ, Dept Genet, Raleigh, NC 27695 USA

来源：

GENOME RESEARCH | 2010年 / 20卷 / 01期

关键词：

MULTIPLE SEQUENCE ALIGNMENT; AMINO-ACID SUBSTITUTIONS; LAC REPRESSOR; PHYLOGENETIC TREES; CRYSTAL-STRUCTURE; CONSERVED DOMAIN; HIV-1; PROTEASE; DATABASE; IDENTIFICATION; FAMILIES;

D O I：

10.1101/gr.097121.109

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：142 / 154

页数：13

共 68 条

[1] Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods [J].

Altenhoff, Adrian M. ;

Dessimoz, Christophe .

PLOS COMPUTATIONAL BIOLOGY, 2009, 5 (01)

[2] ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information [J].

Armon, A ;

Graur, D ;

Ben-Tal, N .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 307 (01) :447-463

[3]

Bell CE, 2000, NAT STRUCT BIOL, V7, P209

[4] ConSeq: the identification of functionally and structurally important residues in protein sequences [J].

Berezin, C ;

Glaser, F ;

Rosenberg, J ;

Paz, I ;

Pupko, T ;

Fariselli, P ;

Casadio, R ;

Ben-Tal, N .

BIOINFORMATICS, 2004, 20 (08) :1322-1324

[5] Alterations in CDH15 and KIRREL3 in Patients with Mild to Severe Intellectual Disability [J].

Bhalla, Kavita ;

Luo, Yue ;

Buchan, Tim ;

Beachem, Michael A. ;

Guzauskas, Gregory F. ;

Ladd, Sydney ;

Bratcher, Shelly J. ;

Schroer, Richard J. ;

Balsamo, Janne ;

DuPont, Barbara R. ;

Lillen, Jack ;

Srivastava, Anand K. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2008, 83 (06) :703-713

[6] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[7] C-cadherin ectodomain structure and implications for cell adhesion mechanisms [J].

Boggon, TJ ;

Murray, J ;

Chappuis-Flament, S ;

Wong, E ;

Gumbiner, BM ;

Shapiro, L .

SCIENCE, 2002, 296 (5571) :1308-1313

[8] Functional classification using phylogenomic inference [J].

Brown, Duncan ;

Sjolander, Kimmen .

PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (06) :479-483

[9] CRYSTAL-STRUCTURE OF A P53 TUMOR-SUPPRESSOR DNA COMPLEX - UNDERSTANDING TUMORIGENIC MUTATIONS [J].

CHO, YJ ;

GORINA, S ;

JEFFREY, PD ;

PAVLETICH, NP .

SCIENCE, 1994, 265 (5170) :346-355

[10]

CRICK F H, 1958, Symp Soc Exp Biol, V12, P138

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