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SNAP predicts effect of mutations on protein function

Yana Bromberg, Guy Yachdav, Burkhard Rost
2008 Computer applications in the biosciences : CABIOS  
Here, we present a publicly available server implementation of the method SNAP (screening for non-acceptable polymorphisms) that predicts the functional effects of single amino acid substitutions.  ...  SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold.  ...  is the raw value of one of the two SNAP output units.  ... 
doi:10.1093/bioinformatics/btn435 pmid:18757876 pmcid:PMC2562009 fatcat:pwowtimxrjgeleyukzydsoouyq

Disease-related mutations predicted to impact protein function

Christian Schaefer, Yana Bromberg, Dominik Achten, Burkhard Rost
2012 BMC Genomics  
Secondly, disease-causing nsSNPs can be identified very well by methods that predict the impact of mutations on protein function.  ...  Most disease-causing mutations were predicted to impact protein function.  ...  This article has been published as part of BMC Genomics Volume 13 Supplement 4, 2012: SNP-SIG 2011: Identification and annotation of SNPs in the context of structure, function and disease.  ... 
doi:10.1186/1471-2164-13-s4-s11 pmid:22759649 pmcid:PMC3394413 fatcat:raugkl3hzffyba56evjqaynutm

Correlating protein function and stability through the analysis of single amino acid substitutions

Yana Bromberg, Burkhard Rost
2009 BMC Bioinformatics  
Results: Here, we analyze to which extent the functional effect of a mutation can be predicted from the effect on protein stability.  ...  However, we also show 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.  ...  and management of mutations.  ... 
doi:10.1186/1471-2105-10-s8-s8 pmid:19758472 pmcid:PMC2745590 fatcat:bktgdmk7j5dx7ktzongd5spk2u

Comprehensive in silico mutagenesis highlights functionally important residues in proteins

Y. Bromberg, B. Rost
2008 Bioinformatics  
Motivation: Mutating residues into alanine (alanine scanning) is one of the fastest experimental means of probing hypotheses about protein function.  ...  Here, we applied SNAP to all experimental mutations in the ASEdb database of alanine scans; we identified 70% of the hot spots (≥1 kCal/mol change in binding energy); more severe changes were predicted  ...  Particular thanks to Guy Yachdav (Columbia) for all his help with setting up and maintaining the SNAP web-server.  ... 
doi:10.1093/bioinformatics/btn268 pmid:18689826 pmcid:PMC2597370 fatcat:s2b3jfyesffg5iupz4y4qdgjri

In silico mutagenesis: a case study of the melanocortin 4 receptor

Yana Bromberg, John Overton, Christian Vaisse, Rudolph L. Leibel, Burkhard Rost
2009 The FASEB Journal  
We applied SNAP, which is a method for quantifying functional consequences of single amino acid (AA) substitutions, to calculate the effects of all possible substitutions at each position in the hMC4R  ...  Here we have performed a complete in silico mutagenesis analysis to assess the functional essentiality of all possible nonnative point mutants in the entire hMC4R protein (332 residues).  ...  A particular pair of aligned residues was predicted either to have the same functional effect (predicted alike) or to have a different effect on function (predicted different).  ... 
doi:10.1096/fj.08-127530 pmid:19417090 pmcid:PMC2735358 fatcat:nnhyvjf7ezbpbfdweefp35kvoa

Neutral and weakly nonneutral sequence variants may define individuality

Y. Bromberg, P. C. Kahn, B. Rost
2013 Proceedings of the National Academy of Sciences of the United States of America  
The second is surprising: the genomes of healthy individuals appear to carry many variants that are predicted to have some effect on function.  ...  Prediction methods indicate that variants in seemingly healthy individuals tend to be neutral or weakly disruptive for protein molecular function.  ...  The work of Y.B. is supported by School of Environmental and Biological Sciences (SEBS), Rutgers University start-up funds. B.R. is supported by the Alexander von Humboldt Foundation.  ... 
doi:10.1073/pnas.1216613110 pmid:23940345 pmcid:PMC3761624 fatcat:ppuigytl75aohoiqmxsfkm5stu

News from the Protein Mutability Landscape

Maximilian Hecht, Yana Bromberg, Burkhard Rost
2013 Journal of Molecular Biology  
The simplest approach predicts all mutations of conserved residues to have an effect; however, this works poorly, at best.  ...  We also discuss how these can be used to improve predictions of protein function and pathogenicity of missense variants.  ...  Some predict the effect on protein function {e.g., sorting intolerant from tolerant (SIFT) [22, 23] or screening for non-acceptable polymorphisms (SNAP) [24, 25] }, others predict the effect with respect  ... 
doi:10.1016/j.jmb.2013.07.028 pmid:23896297 fatcat:puwwuttpvff3vltdg3mqgmjc2i

SNAP: predict effect of non-synonymous polymorphisms on function

Y. Bromberg, B. Rost
2007 Nucleic Acids Research  
Along we introduced SNAP (screening for non-acceptable polymorphisms), a neural network-based method for the prediction of the functional effects of non-synonymous SNPs.  ...  Non-synonymous SNPs are 'neutral' if the resulting point-mutated protein is not functionally discernible from the wild type and 'nonneutral' otherwise.  ...  Leibel (Columbia University) for valuable support, important discussions and the crucial supply of 'real-life' data sets.  ... 
doi:10.1093/nar/gkm238 pmid:17526529 pmcid:PMC1920242 fatcat:4mj3f6af5rg5tcngvg6ecgqrwu

In Silico Screening and Analysis of SNPs in Human ABCB1 (MDR1) Gene [article]

Amira Hussien, Alaa A.M. Osman
2019 bioRxiv   pre-print
PANTHER, SNPs & GO, PhD-SNP, SNAP and PROVEAN confirmed the damaging effects of the first two nsSNPs, while the damaging effect of the third one was predicted only by PhD-SNP and SNAP.  ...  The functional impact of most non-synonymous (ns) SNPs is still unclear. This study adopted a Structural bioinformatics approach to predict the effects of nsSNPs on ABCB1 structure and function.  ...  the functional effects of mutations (PolyPhen, SNAP).  ... 
doi:10.1101/505859 fatcat:np7oijofzzhojea76lxp7on3om

Predict impact of single amino acid change upon protein structure

Christian Schaefer, Burkhard Rost
2012 BMC Genomics  
Amino acid point mutations (nsSNPs) may change protein structure and function. However, no method directly predicts the impact of mutations on structure.  ...  Local structural change can be predicted. Future work will have to establish how useful this new perspective on predicting the effect of nsSNPs will be in combination with other methods.  ...  Particular thanks to the anonymous reviewers and the two editors (Emidio Capriotti, University of Balearic Islands, and Yana Bromberg, Rutgers)  ... 
doi:10.1186/1471-2164-13-s4-s4 pmid:22759652 pmcid:PMC3395892 fatcat:owyz2zarezcf7fui36b5oati2a

Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations [chapter]

Jeannette L. Usher, David B. Ascher, Douglas E. V. Pires, Anna M. Milan, Tom L. Blundell, Lakshminarayan R. Ranganath
2014 JIMD Reports  
Using computational approaches based on the 3D structure, these novel mutations are predicted to affect the activity of the protein complex through destabilisation of the individual protomer structure  ...  A total of 34 sequence variants was observed, confirming the genetic heterogeneity of AKU. Of these mutations, 26 were missense substitutions and four splice site mutations.  ...  Details of the Contributions of Individual Authors JU performed the sequence analysis of the HGD gene mutations, the analysis of the mutations with the freely available bioinformatics programs and the  ... 
doi:10.1007/8904_2014_380 pmid:25681086 pmcid:PMC4582018 fatcat:ew6rdg5aajggrchaxcks5ynxgi

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, IP. Dike
2012 Applied and Translational Genomics  
In order to gain functional insight into mutation caused by amino acid substitution to protein function and expression, special emphasis was laid on molecular dynamics simulation techniques in combination  ...  Majority of mutations predicted by these in silico tools were in good concordance with the experimental results.  ...  Acknowledgments The authors take this opportunity to thank the management of VIT University for providing the facilities and encouragement to carry out this work.  ... 
doi:10.1016/j.atg.2012.06.002 pmid:27896051 pmcid:PMC5121281 fatcat:d2dqdx6sr5a2rntgbgoknutfze

Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia

Dwi Wulandari, Lisnawati Rachmadi, Tjahjani M. Sudiro
2015 Medical Journal of Indonesia  
Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.  ...  The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function.  ...  Acknowledgment The authors would like to acknowledge Ulima Darmania Amanda, S.Si at the Department of Pathological Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta for maintaining material  ... 
doi:10.13181/mji.v24i4.1197 fatcat:3h2piepz2vfrzfyrsdiyufdtty

Prediction of the Effects of Missense Mutations on Human Myeloperoxidase Protein Stability Using In Silico Saturation Mutagenesis

Adebiyi Sobitan, William Edwards, Md Shah Jalal, Ayanfeoluwa Kolawole, Hemayet Ullah, Atanu Duttaroy, Jiang Li, Shaolei Teng
2022 Genes  
Our computational tool prediction showed the destabilizing effects in 13 out of 14 MPO missense mutations that cause diseases in humans.  ...  We utilized in silico saturation mutagenesis to generate and analyze the effects of 10,811 potential missense mutations on MPO stability.  ...  This project research was supported (in part) by the Howard University startup funds (U100193), the National Science Foundation (IIS 1924092), and the National Institute on Minority Health and Health Disparities  ... 
doi:10.3390/genes13081412 pmid:36011324 pmcid:PMC9407467 fatcat:aigfc3lg2jbn5lpkg64zfw7fva

Evolution- and Structure-Based Computational Strategy Reveals the Impact of Deleterious Missense Mutations on MODY 2 (Maturity-Onset Diabetes of the Young, Type 2)

Doss C. Priya George, Chiranjib Chakraborty, SA Syed Haneef, Nagarajan NagaSundaram, Luonan Chen, Hailong Zhu
2014 Theranostics  
Based on the computational prediction scores obtained using these methods, three mutations, namely E70K, A188T, and W257R, were identified as highly deleterious on the basis of their effects on protein  ...  The effects of the mutations on protein stability were computed using PoPMusic 2.1, I-mutant 3.0, and Dmutant.  ...  In this method, a probability score greater than 0.5 predicts that the mutation will have a disease-related effect on the parent protein function.  ... 
doi:10.7150/thno.7473 pmid:24578721 pmcid:PMC3936290 fatcat:p5mqwl2zhzcv5omcum2xg2n4by
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