firestar —advances in the prediction of functionally important residues

Lopez, Gonzalo; Maietta, Paolo; Rodriguez, José Manuel; Valencia, Alfonso; Tress, Michael L.

doi:10.1093/nar/gkr437

Cited by 53 publications

(48 citation statements)

References 21 publications

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“…To examine the sensitivity of our method of identifying functional residues in PB1, we performed a thorough literature search, compiled 31 residues that were reported to be functional in PB1 (32, 51–54), and compared the performance of our method with that of four other methods: FireStar, Frpreq, Consurf, and Concavity (6, 10, 55–58) (Table 1). Our method was able to identify 21 of the 31 residues and thus had a sensitivity of ~68%.…”

Section: Resultsmentioning

confidence: 99%

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

Jiang

et al. 2016

mBio

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Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.

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Section: Resultsmentioning

confidence: 99%

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

Jiang

et al. 2016

mBio

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“…• firestar (Lopez et al 2007(Lopez et al , 2011) is a method that predicts functionally important residues in protein sequences.…”

Section: Appris (Cnio)mentioning

confidence: 99%

GENCODE: The reference human genome annotation for The ENCODE Project

et al. 2012

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The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE proteincoding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

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“…Splice isoforms in APPRIS are annotated with protein structural information via mapping to structural homologues and with functional information from the conserved, functionally important amino acid residues predicted by firestar 28 and from Pfam functional domains. 29 The conservation information used to select principal isoforms comes from protein alignments between vertebrate orthologues.…”

Section: Principal Splice Isoformsmentioning

confidence: 99%

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

et al. 2015

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Although eukaryotic cells express a wide range of alternatively spliced transcripts, it is not clear whether genes tend to express a range of transcripts simultaneously across cells, or produce dominant isoforms in a manner that is either tissue-specific or regardless of tissue. To date, large-scale investigations into the pattern of transcript expression across distinct tissues have produced contradictory results. Here, we attempt to determine whether genes express a dominant splice variant at the protein level. We interrogate peptides from eight large-scale human proteomics experiments and databases and find that there is a single dominant protein isoform, irrespective of tissue or cell type, for the vast majority of the protein-coding genes in these experiments, in partial agreement with the conclusions from the most recent large-scale RNAseq study. Remarkably, the dominant isoforms from the experimental proteomics analyses coincided overwhelmingly with the reference isoforms selected by two completely orthogonal sources, the consensus coding sequence variants, which are agreed upon by separate manual genome curation teams, and the principal isoforms from the APPRIS database, predicted automatically from the conservation of protein sequence, structure, and function.

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firestar —advances in the prediction of functionally important residues

Cited by 53 publications

References 21 publications

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

GENCODE: The reference human genome annotation for The ENCODE Project

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

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