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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Predictors of parkin mutations in early-onset Parkinson disease: the consortium on risk for early-onset Parkinson disease study.
Karen Marder,Ming X. Tang,Helen Mejia-Santana,Llency Rosado,Elan D. Louis,Cynthia L. Comella,Amy Colcher,Andrew Siderowf,Danna Jennings,Martha Nance,Susan B. Bressman,William K. Scott,Caroline M. Tanner,Susan F. Mickel,Howard Andrews,Cheryl Waters,Stanley Fahn,Barbara Ross,Lucien J. Cote,Steven J. Frucht,Blair Ford,Roy N. Alcalay,Michael Rezak,Michael Rezak,Kevin Novak,Kevin Novak,Joseph H. Friedman,Ronald F. Pfeiffer,Laura Marsh,Brad Hiner,Gregory D. Neils,Miguel Verbitsky,Sergey Kisselev,Elise Caccappolo,Ruth Ottman,Lorraine N. Clark +35 more
TL;DR: Age at onset, Hispanic race/ethnicity, and family history of PD are associated with carrying any parkin mutation (heterozygous, homozygous) or compound heterozygous parkin mutations alone, and the increased odds of carrying a parkin mutated among Hispanics warrants further study.
Journal ArticleDOI
A novel mutation in JARID1C gene associated with mental retardation.
Cristina Santos,Laia Rodriguez-Revenga,Irene Madrigal,Celia Badenas,Mercè Pineda,Montserrat Milà +5 more
TL;DR: This work describes the results obtained by screening JARID1C gene in 24 mentally retarded males with history of at least two affected males and finds a novel missense mutation in exon 10 of the gene that results in a Serine-to-arginine change at amino-acid 451 (S451R).
Journal ArticleDOI
Correlating protein function and stability through the analysis of single amino acid substitutions
Yana Bromberg,Burkhard Rost +1 more
TL;DR: It is confirmed that stability change is somehow related to function change, but it is also shown that the knowledge of stability changes in no way suffices to predict functional changes and that many function changing mutations have no effect on stability.
Journal ArticleDOI
Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species.
Michael Lang,Sophie Murat,Sophie Murat,Andrew G. Clark,Géraldine Gouppil,Catherine Blais,Luciano M. Matzkin,Emilie Guittard,Takuji Yoshiyama-Yanagawa,Takuji Yoshiyama-Yanagawa,Hiroshi Kataoka,Ryusuke Niwa,René Lafont,Chantal Dauphin-Villemant,Virginie Orgogozo,Virginie Orgogozo +15 more
TL;DR: How relatively few genetic changes in a single gene may restrict the ecological niche of a species is illustrated by the dependence of Drosophila pachea on its single host, the senita cactus.
Journal ArticleDOI
Learning Rich Part Hierarchies With Progressive Attention Networks for Fine-Grained Image Recognition
TL;DR: Zhang et al. as mentioned in this paper proposed a progressive-attention convolutional neural network (PA-CNN) to progressively localize parts at multiple scales, where a part proposal network (PPN) generates multiple local attention maps and a part rectification network (PRN) learns part-specific features from each proposal and provides the PPN with refined part locations.
References
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Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
Journal ArticleDOI
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
Amos Marc Bairoch,Rolf Apweiler +1 more
TL;DR: The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
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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.