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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Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment
Evan S. Snitkin,Adrian M. Zelazny,Jyoti Gupta,Tara N. Palmore,Patrick R. Murray,Julia A. Segre +5 more
TL;DR: This study provides a unique window into mutational pathways taken in response to antibiotic pressure in vivo, and demonstrates the potential for genome sequence data to predict resistance phenotypes.
Journal ArticleDOI
Disease mutations in disordered regions—exception to the rule?
TL;DR: It is argued that disease-associated missense mutations located in the intrinsically disordered regions are more prevalent and have larger functional impact than previously thought, and it is demonstrated that deleterious amino acid substitutions that cause disorder-to-order transitions are particularly enriched among disease mutations compared to neutral polymorphisms.
Journal ArticleDOI
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins.
Daniele Raimondi,Daniele Raimondi,Ibrahim Tanyalcin,Julien Ferte,Andrea Gazzo,Gabriele Orlando,Gabriele Orlando,Tom Lenaerts,Tom Lenaerts,Marianne Rooman,Wim F. Vranken +10 more
TL;DR: In this paper, the authors present a method, DEOGEN2, which incorporates heterogeneous information about the molecular effects of the variants, the domains involved, the relevance of the gene and the interactions in which it participates.
Journal ArticleDOI
Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning
Stephanie N. Dorman,Katherina Baranova,Joan H.M. Knoll,Joan H.M. Knoll,Brad L. Urquhart,Gabriella Mariani,Maria Luisa Carcangiu,Peter K. Rogan +7 more
TL;DR: Investigation of correspondence between growth inhibitory concentrations of paclitaxel and gemcitabine and gene copy number, mutation, and expression first in breast cancer cell lines and then in patients found patterns related to changes in the genomic profile of tumors.
Journal ArticleDOI
Molecular basis of antithrombin deficiency
Beate Luxembourg,D. Delev,Christof Geisen,Michael Spannagl,Manuela Krause,Wolfgang Miesbach,Christine Heller,Frauke Bergmann,Ursula Schmeink,Ralf Grossmann,Edelgard Lindhoff-Last,Erhard Seifried,Johannes Oldenburg,Anna Pavlova +13 more
TL;DR: Characterisation of the SERPINC1 mutation profile in large cohorts of patients may help to further elucidate the pathogenesis of AT deficiency and to establish genotype-phenotype associations.
References
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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.