Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

[1]  Hagen U. Tilgner,et al.  Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome , 2018, Genome research.

[2]  David L. Gibbs,et al.  The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research. , 2017, Cancer research.

[3]  Pascal Borry,et al.  Reporting practices for variants of uncertain significance from next generation sequencing technologies. , 2017, European journal of medical genetics.

[4]  John C. Earls,et al.  A wellness study of 108 individuals using personal, dense, dynamic data clouds , 2017, Nature Biotechnology.

[5]  Moriah H Nissan,et al.  OncoKB: A Precision Oncology Knowledge Base. , 2017, JCO precision oncology.

[6]  P. Stenson,et al.  The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies , 2017, Human Genetics.

[7]  P. Stenson,et al.  The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies , 2017, Human Genetics.

[8]  Christopher J. Richardson,et al.  Identification and analysis of mutational hotspots in oncogenes and tumour suppressors , 2017, Oncotarget.

[9]  Wei Zheng,et al.  BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts. , 2017, Journal of molecular biology.

[10]  Steven J. M. Jones,et al.  CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer , 2017, Nature Genetics.

[11]  Mingming Jia,et al.  COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..

[12]  Marcin Imielinski,et al.  The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations , 2016, J. Am. Medical Informatics Assoc..

[13]  Hannah Carter,et al.  CRAVAT: cancer-related analysis of variants toolkit , 2013, Bioinform..

[14]  張正儀,et al.  基於Google Cloud Platform設計高效能日誌分析平台之研究 , 2017 .

[15]  said John Heymach Modeling Cancer Mutations in 3-D. , 2017, Cancer discovery.

[16]  C. Sander,et al.  3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets , 2017, Genome Medicine.

[17]  Yang Zhang,et al.  STRUM: structure-based prediction of protein stability changes upon single-point mutation , 2016, Bioinform..

[18]  Piero Fariselli,et al.  INPS-MD: a web server to predict stability of protein variants from sequence and structure , 2016, Bioinform..

[19]  Douglas E. V. Pires,et al.  mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance , 2016, Scientific Reports.

[20]  David L. Masica,et al.  Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure. , 2016, Cancer research.

[21]  Raymond Dalgleish,et al.  HGVS Recommendations for the Description of Sequence Variants: 2016 Update , 2016, Human mutation.

[22]  Douglas E. V. Pires,et al.  mCSM-AB: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures , 2016, Nucleic Acids Res..

[23]  Joan Teyra,et al.  ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity , 2016, Bioinform..

[24]  Anna R. Panchenko,et al.  MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions , 2016, Nucleic Acids Res..

[25]  Andreas Keller,et al.  StructMAn: annotation of single-nucleotide polymorphisms in the structural context , 2016, Nucleic Acids Res..

[26]  Johannes Söding,et al.  The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis , 2016, Nucleic Acids Res..

[27]  E. Alexov,et al.  SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations , 2016, International journal of molecular sciences.

[28]  E. Alexov,et al.  SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach , 2016, International journal of molecular sciences.

[29]  Jeffrey Skolnick,et al.  ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures , 2016, PloS one.

[30]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[31]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, bioRxiv.

[32]  Richard Bonneau,et al.  Robust classification of protein variation using structural modelling and large-scale data integration , 2015, bioRxiv.

[33]  Gustavo Glusman,et al.  Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals , 2016, Human Genome Variation.

[34]  Ricardo Villamarín-Salomón,et al.  ClinVar: public archive of interpretations of clinically relevant variants , 2015, Nucleic Acids Res..

[35]  James Y. Zou Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[36]  Heidi L. Rehm,et al.  Building the foundation for genomics in precision medicine , 2015, Nature.

[37]  Yang Zhang,et al.  Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles , 2015, PLoS Comput. Biol..

[38]  Subha Madhavan,et al.  SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures , 2015, Computational and structural biotechnology journal.

[39]  David D. Shteynberg,et al.  State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. , 2015, Journal of proteome research.

[40]  J. Skolnick,et al.  Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. , 2015, Structure.

[41]  Amber M. Johnson,et al.  A decision support framework for genomically informed investigational cancer therapy. , 2015, Journal of the National Cancer Institute.

[42]  Michele Magrane,et al.  Searching and Navigating UniProt Databases , 2015, Current protocols in bioinformatics.

[43]  Zhao Zhang,et al.  Rethinking Data-Intensive Science Using Scalable Analytics Systems , 2015, SIGMOD Conference.

[44]  T. Blauwkamp,et al.  Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events , 2015, Nature Biotechnology.

[45]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[46]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[47]  Martin Eisenacher,et al.  Development of data representation standards by the human proteome organization proteomics standards initiative , 2015, J. Am. Medical Informatics Assoc..

[48]  Mauno Vihinen,et al.  VariSNP, A Benchmark Database for Variations From dbSNP , 2015, Human mutation.

[49]  K. Tomczak,et al.  The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge , 2015, Contemporary oncology.

[50]  Adam Godzik,et al.  Cancer3D: understanding cancer mutations through protein structures , 2014, Nucleic Acids Res..

[51]  Douglas E. V. Pires,et al.  Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes , 2014, Nucleic Acids Res..

[52]  Angela D. Wilkins,et al.  Single nucleotide variations: Biological impact and theoretical interpretation , 2014, Protein science : a publication of the Protein Society.

[53]  M. Sternberg,et al.  SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features , 2014, Journal of molecular biology.

[54]  Douglas E. V. Pires,et al.  DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach , 2014, Nucleic Acids Res..

[55]  Marco Biasini,et al.  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information , 2014, Nucleic Acids Res..

[56]  Greg Gibson,et al.  SDS, a structural disruption score for assessment of missense variant deleteriousness , 2014, Front. Genet..

[57]  Karin S Kassahn,et al.  Integrating Massively Parallel Sequencing into Diagnostic Workflows and Managing the Annotation and Clinical Interpretation Challenge , 2014, Human mutation.

[58]  Douglas E. V. Pires,et al.  mCSM: predicting the effects of mutations in proteins using graph-based signatures , 2013, Bioinform..

[59]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[60]  Torsten Schwede,et al.  Protein modeling: what happened to the "protein structure gap"? , 2013, Structure.

[61]  M. Diekhans,et al.  MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures , 2013, Human Genetics.

[62]  Marianne Rooman,et al.  BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations , 2013, Nucleic Acids Res..

[63]  Juergen Haas,et al.  The Protein Model Portal—a comprehensive resource for protein structure and model information , 2013, Database J. Biol. Databases Curation.

[64]  Gustavo Glusman,et al.  Clinical applications of sequencing take center stage , 2013, Genome Biology.

[65]  Mauno Vihinen,et al.  VariBench: A Benchmark Database for Variations , 2013, Human mutation.

[66]  Maria Jesus Martin,et al.  SIFTS: Structure Integration with Function, Taxonomy and Sequences resource , 2012, Nucleic Acids Res..

[67]  Chao Chen,et al.  dbVar and DGVa: public archives for genomic structural variation , 2012, Nucleic Acids Res..

[68]  Juan Fernández-Recio,et al.  SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models , 2012, Bioinform..

[69]  Matthew B. Callaway,et al.  MuSiC: Identifying mutational significance in cancer genomes , 2012, Genome research.

[70]  Olivier Poch,et al.  KD4v: comprehensible knowledge discovery system for missense variant , 2012, Nucleic Acids Res..

[71]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[72]  Joaquín Dopazo,et al.  SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants , 2011, Nucleic Acids Res..

[73]  Jared C. Roach,et al.  Kaviar: an accessible system for testing SNV novelty , 2011, Bioinform..

[74]  Russ B. Altman,et al.  Improving the prediction of disease-related variants using protein three-dimensional structure , 2011, BMC Bioinformatics.

[75]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[76]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[77]  Catherine L. Worth,et al.  SDM—a server for predicting effects of mutations on protein stability and malfunction , 2011, Nucleic Acids Res..

[78]  D. Baker,et al.  Role of conformational sampling in computing mutation‐induced changes in protein structure and stability , 2011, Proteins.

[79]  Jens Meiler,et al.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.

[80]  Majid Masso,et al.  AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements. , 2010, Protein engineering, design & selection : PEDS.

[81]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[82]  Yun Liu,et al.  LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures , 2009, Bioinform..

[83]  Yang Zhang Protein structure prediction: when is it useful? , 2009, Current opinion in structural biology.

[84]  L. Hood,et al.  Systems medicine: the future of medical genomics and healthcare , 2009, Genome Medicine.

[85]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[86]  Yang Zhang Progress and challenges in protein structure prediction. , 2008, Current opinion in structural biology.

[87]  Bala Krishnamoorthy,et al.  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm481 Structural bioinformatics Four-Body Scoring Function for Mutagenesis , 2007 .

[88]  M. Michael Gromiha,et al.  CUPSAT: prediction of protein stability upon point mutations , 2006, Nucleic Acids Res..

[89]  Marc A. Martí-Renom,et al.  MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..

[90]  Akinori Sarai,et al.  ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions , 2005, Nucleic Acids Res..

[91]  Arlo Z. Randall,et al.  Prediction of protein stability changes for single‐site mutations using support vector machines , 2005, Proteins.

[92]  François Stricher,et al.  The FoldX web server: an online force field , 2005, Nucleic Acids Res..

[93]  Piero Fariselli,et al.  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure , 2005, Nucleic Acids Res..

[94]  Nichole L. King,et al.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry , 2004, Genome Biology.

[95]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[96]  Russ B. Altman,et al.  MutDB: annotating human variation with functionally relevant data , 2003, Bioinform..

[97]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[98]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[99]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..