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
More filters
Journal ArticleDOI
High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE.
Stefano Castellana,Caterina Fusilli,Gianluigi Mazzoccoli,Tommaso Biagini,Daniele Capocefalo,Massimo Carella,Angelo L. Vescovi,Tommaso Mazza +7 more
TL;DR: APOGEE, a machine-learning algorithm that outperforms all existing prediction methods in estimating the harmfulness of mitochondrial non-synonymous genome variations, is designed and implemented.
Journal ArticleDOI
Evidence for several independent genetic variants affecting lipoprotein (a) cholesterol levels
Wensheng Lu,Yu-Ching Cheng,Keping Chen,Hong Wang,Glenn S. Gerhard,Christopher D. Still,Xin Chu,Rongze Yang,Ankita Parihar,Jeffrey R. O'Connell,Toni I. Pollin,Eduardo Anglés-Cano,Michael J. Quon,Braxton D. Mitchell,Alan R. Shuldiner,Mao Fu +15 more
TL;DR: A genome-wide association scan to identify genetic variants associated with Lp(a)-cholesterol levels in the Old Order Amish found a previously known locus on chromosome 6q25-26 and found Lp (a) levels also to be significantly associated with a SNP near the APOA5-APOA4-APOC3- APOA1 gene cluster on chromosome 11q23 linked in the Amish to the APOC3 R19X null mutation.
Journal ArticleDOI
Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach.
C. George Priya Doss,N. Nagasundaram,Chiranjib Chakraborty,Chiranjib Chakraborty,Luonan Chen,Luonan Chen,Hailong Zhu +6 more
TL;DR: A theoretical assessment for the discovery of new drugs or drug targets in CDK7 protein owing to the changes caused by deleterious nsSNPs is described and the identification of disease related SNPs by computational methods has the potential to create personalized tools for the diagnosis, prognosis, and treatment of diseases.
Journal ArticleDOI
Hansa: an automated method for discriminating disease and neutral human nsSNPs.
TL;DR: A support vector machine (SVM) based method named Hansa which uses a novel set of discriminatory features to classify nsSNPs into disease (pathogenic) and benign (neutral) types and shows that Hansa outperforms the other known methods.
Journal ArticleDOI
Intellectual disability and bleeding diathesis due to deficient CMP--sialic acid transport.
Miski Mohamed,Angel Ashikov,Maïlys Guillard,Joris H. Robben,Samuel Schmidt,B. van den Heuvel,Arjan P.M. de Brouwer,Rita Gerardy-Schahn,Peter M.T. Deen,Ron A. Wevers,Dirk Lefeber,Eva Morava +11 more
TL;DR: The primary neurologic presentation consisting of ataxia, intellectual disability, and seizures, in combination with bleeding diathesis and proteinuria, is discriminative from a previous case described with deficient sialic acid transporter and underlines the importance of sialylation for normal CNS development and regular organ function.
References
More filters
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.
Journal ArticleDOI
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.