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The UCSC Genome Browser database: update 2010

B. Rhead, D. Karolchik, R. M. Kuhn, A. S. Hinrichs, A. S. Zweig, P. A. Fujita, M. Diekhans, K. E. Smith, K. R. Rosenbloom, B. J. Raney, A. Pohl, M. Pheasant (+11 others)
2009 Nucleic Acids Research  
and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.  ...  set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data.  ...  ACKNOWLEDGEMENTS We wish to thank the numerous collaborators worldwide who have contributed annotation data to the Genome Browser, the individuals on our Scientific Advisory Board who guide our work, and  ... 
doi:10.1093/nar/gkp939 pmid:19906737 pmcid:PMC2808870 fatcat:k3rf3riiznfexe3h7ydbhitysi

Impact of genetic variation on three dimensional structure and function of proteins

Roshni Bhattacharya, Peter W. Rose, Stephen K. Burley, Andreas Prlić, Yang Zhang
2017 PLoS ONE  
The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings.  ...  Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation  ...  LS-SNP/PDB: Annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 2009; 25(11):1431-2. https://doi.org/10.1093/ bioinformatics/btp242 PMID: 19369493 35.  ... 
doi:10.1371/journal.pone.0171355 pmid:28296894 pmcid:PMC5351996 fatcat:fu6vzdo4hjdrliuimow2h56xe4

Candidate gene association studies: a comprehensive guide to useful in silico tools

Radhika Patnala, Judith Clements, Jyotsna Batra
2013 BMC Genetics  
LS-SNP/PDB (http://ls-snp.icm.jhu.edu/ls-snp-pdb/) [66] lets one map the variations on 3D structures available in Protein Data Bank.  ...  SNPs in the coding region which leads to a change in the translated amino acids and thus in the encoded protein are categorised as non-synonymous SNPs (nsSNPs), as encoded protein sequences differ between  ...  Submit your next manuscript to BioMed Central and take full advantage of:  ... 
doi:10.1186/1471-2156-14-39 pmid:23656885 pmcid:PMC3655892 fatcat:gexwqedhvzgihmclq7pqdwqsri

Bioinformatics for personal genome interpretation

E. Capriotti, N. L. Nehrt, M. G. Kann, Y. Bromberg
2012 Briefings in Bioinformatics  
Many resources aim to identify and annotate the specific genes responsible for the observed phenotypes.  ...  This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants  ...  Acknowledgements We acknowledge all the colleagues who contributed in the organization and panel discussions at the last PSB and ISMB SNP-SIG meetings.  ... 
doi:10.1093/bib/bbr070 pmid:22247263 pmcid:PMC3404395 fatcat:zdu5z4bbtncerp7cyw6mjrf3d4

FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases

Stephen J Goodswen, Cedric Gondro, Nathan S Watson-Haigh, Haja N Kadarmideen
2010 BMC Bioinformatics  
The local relational databases contain SNP data together with functional annotations extracted from online resources.  ...  FunctSNP is unique in that it is the only R package that links SNPs to functional annotation.  ...  Special thanks to Professor Julius van der Werf (University of New England) who provided helpful guidance and manuscript editing. Author Details  ... 
doi:10.1186/1471-2105-11-311 pmid:20534127 pmcid:PMC2901372 fatcat:ehj7pcnyyjfaxbgfaoo7ayvpwy

PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
2022 Journal of Cheminformatics  
For example, developing machine learning algorithms to predict protein–ligand affinity or a SNP effect on it requires an extensive amount of data.  ...  It provides a web interface to explore and visualize the protein–ligand complexes and a REST API to programmatically access the different aspects of the database contents.  ...  SwissVar and dbSNP are the main sources of SNPs PinSnps [15] 2013 Exploring the impact of SNPs on Protein Domains and Complexes LS-SNP/PDB [16] 2009, Not available anymore G23D [17] 2016, Not downloadable  ... 
doi:10.1186/s13321-021-00573-5 pmid:35227289 pmcid:PMC8886843 fatcat:mac7atc7kzb4hk7lbimzzkd5z4

In SilicoPrediction of the Effects of Mutations in the Human Mevalonate Kinase Gene: Towards a Predictive Framework for Mevalonate Kinase Deficiency

Claire Browne, David J. Timson
2015 Annals of Human Genetics  
. & Karchin, R. (2009) LS-SNP/PDB: annotated non-synonymous 24 SNPs mapped to Protein Data Bank structures.  ...  Thus, all structural comparisons were made using 40 41 minimised structures. Each variant's structure was further analysed using LS-SNP/PDB (http://ls- 42 43 snp.icm.jhu.edu/ls-snp-pdb/main).  ... 
doi:10.1111/ahg.12126 pmid:26420133 fatcat:3tlnwgcv7nfpnppx2qsjpityma

The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer

Saliha Ece Acuner Ozbabacan, Attila Gursoy, Ruth Nussinov, Ozlem Keskin, Yu Xia
2014 PLoS Computational Biology  
By predicting the protein-protein complexes throughout the pathway via the PRISM algorithm, the structural coverage increases from 15% to 71%.  ...  Computational mapping of mutations on the interface of the predicted complexes may constitute a powerful strategy to explain the mechanisms of activation/inhibition.  ...  The list of SNPs and mutations related to the target proteins is obtained from LS-SNP/PDB which is a web tool for genome-wide annotations of human non-synonymous SNPs mapped to Protein Data Bank structures  ... 
doi:10.1371/journal.pcbi.1003470 pmid:24550720 pmcid:PMC3923659 fatcat:kkruh5ugdfcrjkrqz4fx7qebui

Bioinformatics and variability in drug response: a protein structural perspective

J. L. Lahti, G. W. Tang, E. Capriotti, T. Liu, R. B. Altman
2012 Journal of the Royal Society Interface  
Together these advances provide the opportunity to examine how altered protein structures arising from genetic differences affect protein -drug interactions and, ultimately, drug response.  ...  Over the past decade, progress in structural genomics led to an explosion of available three-dimensional structures of drug target proteins while efforts in pharmacogenetics offered insights into polymorphisms  ...  structures LS-SNP [295] http://ls-snp.icm.jhu.edu/ls-snp-pdb VnD [296] http://vandd.org SuperCYP [297] http://bioinformatics.charite.de/supercyp genetic variants and drug response PharmGKB [298  ... 
doi:10.1098/rsif.2011.0843 pmid:22552919 pmcid:PMC3367825 fatcat:olvu5dx4rnaahpeadr6yhntwau

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

Tugba Kucukkal, Ye Yang, Susan Chapman, Weiguo Cao, Emil Alexov
2014 International Journal of Molecular Sciences  
expressed proteins.  ...  DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and  ...  All authors contributed to the Case Study section.  ... 
doi:10.3390/ijms15069670 pmid:24886813 pmcid:PMC4100115 fatcat:wvilvvfkmfbz3owuys6qjz4npq

Protein-structure-guided discovery of functional mutations across 19 cancer types

Beifang Niu, Adam D Scott, Sohini Sengupta, Matthew H Bailey, Prag Batra, Jie Ning, Matthew A Wyczalkowski, Wen-Wei Liang, Qunyuan Zhang, Michael D McLellan, Sam Q Sun, Piyush Tripathi (+7 others)
2016 Nature Genetics  
We developed a computational tool, HotSpot3D, to identify such spatial hotspots (clusters) and to interpret the potential function of variants within them.  ...  However, their 3dimensional (3D) spatial relationships have yet to be systematically explored.  ...  We thank Kimberly Johnson, Cyriac Kandoth, Maheetha Bharadwaj, and Kuan-lin Huang for suggestions on data analysis.  ... 
doi:10.1038/ng.3586 pmid:27294619 pmcid:PMC5315576 fatcat:nwtjc6bvl5ewrbes3zuc65jzgm