SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng,Steven Henikoff +1 more
TLDR
SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study and can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms.Abstract:
Single nucleotide polymorphism (SNP) studies and random mutagenesis projects identify amino acid substitutions in protein-coding regions. Each substitution has the potential to affect protein function. SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study. We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html.read more
Citations
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Differentially Expressed Genes in Endometrium and Corpus Luteum of Holstein Cows Selected for High and Low Fertility Are Enriched for Sequence Variants Associated with Fertility
S.G. Moore,S.G. Moore,Jennie E. Pryce,Ben J. Hayes,Amanda J. Chamberlain,Kathryn E. Kemper,Donagh P. Berry,Matthew S. McCabe,Paul Cormican,Patrick Lonergan,Trudee Fair,S. T. Butler +11 more
TL;DR: The results of this study enhance the understanding of the contribution of the endometrium and corpus luteum transcriptome to phenotypic fertility differences and the genetic architecture of fertility in dairy cattle.
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Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications.
Gholson J. Lyon,Tao Jiang,Richard van Wijk,Wei Wang,Paul Bodily,Jinchuan Xing,Lifeng Tian,Reid J. Robison,Mark J. Clement,Yang Lin,Peng Zhang,Ying Liu,Barry Moore,Joseph T. Glessner,Josephine Elia,Frederick W. Reimherr,Wouter W. van Solinge,Mark Yandell,Hakon Hakonarson,Jun Wang,William Evan Johnson,Zhi Wei,Kai Wang +22 more
TL;DR: This study implies that exome and genome sequencing will certainly reveal additional rare variation causative for even well-studied classical Mendelian diseases, while also revealing variants that might play a role in complex diseases.
Journal ArticleDOI
Screening of mutations affecting protein stability and dynamics of FGFR1-A simulation analysis.
C. George Priya Doss,B. Rajith,Nimisha Garwasis,Pretty Raju Mathew,Anand Solomon Raju,K Apoorva,Denise William,N R Sadhana,Tanwar Himani,I P Dike +9 more
TL;DR: Molecular dynamics approach has shown that P722S mutation leads to increase in flexibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds, and biophysical analysis revealed a clear insight of stability loss due to P7 22S mutation in FGFR1 protein.
Journal ArticleDOI
The SAAPdb web resource: a large-scale structural analysis of mutant proteins.
Jacob Hurst,Lisa E. M. McMillan,Craig T. Porter,James E. Allen,Adebola Fakorede,Andrew J. Martin +5 more
TL;DR: An analysis of the contents of SAAPdb indicates that there are clear differences in the sequence and structural characteristics of SNPs and PDs, and that PDs are more often explained by the authors' structural analysis.
Journal ArticleDOI
A patient-derived-xenograft platform to study BRCA-deficient ovarian cancers
Erin George,Hyoung Kim,Clemens Krepler,Brandon Wenz,Mehran Makvandi,Janos L. Tanyi,Eric J. Brown,Rugang Zhang,Patricia Brafford,Stephanie Jean,Robert H. Mach,Yiling Lu,Gordon B. Mills,Meenhard Herlyn,Mark A. Morgan,Xiaochen Zhang,Robert A. Soslow,Ronny Drapkin,Neil Johnson,Ying Zheng,George Cotsarelis,Katherine L. Nathanson,Fiona Simpkins,Fiona Simpkins +23 more
TL;DR: The orthotopic H GSOC PDX model represents a robust and reliable model to optimize therapeutic strategies for BRCAMUT HGSOC, indicating retention of underlying molecular mechanisms of carcinogenesis.
References
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Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
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Predicting Deleterious Amino Acid Substitutions
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: A tool that uses sequence homology to predict whether a substitution affects protein function is constructed, which may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.
Journal ArticleDOI
Human non‐synonymous SNPs: server and survey
TL;DR: A World Wide Web server is presented to predict the effect of an nsSNP on protein structure and function and the dependence of selective pressure on the structural and functional properties of proteins is studied.