Refining Transcriptome Gene Catalogs by MS‐Validation of Expressed Proteins
Sign Up to like & getrecommendations! Published in 2018 at "PROTEOMICS"
DOI: 10.1002/pmic.201700271
Abstract: Protein sequence identification by tandem mass spectroscopy (LC‐MS/MS) identifies thousands of protein sequences even in complex mixtures, and provides valuable insight into the biological functions of different cells. For non‐model organisms, transcriptomes are generally used… read more here.
Keywords: protein; validated protein; protein sequence; protein sequences ... See more keywords
High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8736-8_8
Abstract: Ancestral protein sequence reconstruction is a powerful technique for explicitly testing hypotheses about the evolution of molecular function, allowing researchers to meticulously dissect how historical changes in protein sequence impacted functional repertoire by altering the… read more here.
Keywords: reconstruction; protein sequence; structure; function ... See more keywords
Protein Sequence Editing of SKN-1A/Nrf1 by Peptide:N-Glycanase Controls Proteasome Gene Expression
Sign Up to like & getrecommendations! Published in 2019 at "Cell"
DOI: 10.1016/j.cell.2019.03.035
Abstract: The proteasome mediates selective protein degradation and is dynamically regulated in response to proteotoxic challenges. SKN-1A/Nrf1, an endoplasmic reticulum (ER)-associated transcription factor that undergoes N-linked glycosylation, serves as a sensor of proteasome dysfunction and triggers… read more here.
Keywords: sequence editing; protein sequence; peptide glycanase; skn nrf1 ... See more keywords
An alignment-free measure based on physicochemical properties of amino acids for protein sequence comparison
Sign Up to like & getrecommendations! Published in 2019 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2019.01.005
Abstract: Sequence comparison is an important topic in bioinformatics. With the exponential increase of biological sequences, the traditional protein sequence comparison methods - the alignment methods become limited, so the alignment-free methods are widely proposed in… read more here.
Keywords: sequence comparison; physicochemical properties; protein sequence; alignment free ... See more keywords
Considerations for constructing a protein sequence database for metaproteomics
Sign Up to like & getrecommendations! Published in 2022 at "Computational and Structural Biotechnology Journal"
DOI: 10.1016/j.csbj.2022.01.018
Abstract: Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of… read more here.
Keywords: sequence; sequence database; database; construction ... See more keywords
A novel model for protein sequence similarity analysis based on spectral radius
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Theoretical Biology"
DOI: 10.1016/j.jtbi.2018.03.001
Abstract: Abstract Advances in sequencing technologies led to rapid increase in the number and diversity of biological sequences, which facilitated development in the sequence research. In this paper, we present a new method for analyzing protein… read more here.
Keywords: similarity; analysis; protein sequence; sequence similarity ... See more keywords
Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.8b00404
Abstract: The Chromosome-centric Human Proteome Project (C-HPP) seeks to comprehensively characterize all protein products coded by the genome, including those expressed sequence variants confirmed via proteogenomics methods. The closely related Biology/Disease-driven Human Proteome Project (B/D-HPP) seeks… read more here.
Keywords: via proteogenomics; human proteome; protein sequence; sequence variants ... See more keywords
Mathematical Approach to Protein Sequence Comparison Based on Physiochemical Properties
Sign Up to like & getrecommendations! Published in 2022 at "ACS Omega"
DOI: 10.1021/acsomega.2c06103
Abstract: The difficult aspect of developing new protein sequence comparison techniques is coming up with a method that can quickly and effectively handle huge data sets of various lengths in a timely manner. In this work,… read more here.
Keywords: protein sequence; property; sequence comparison; comparison ... See more keywords
Protein sequence design with a learned potential
Sign Up to like & getrecommendations! Published in 2022 at "Nature Communications"
DOI: 10.1038/s41467-022-28313-9
Abstract: The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of… read more here.
Keywords: design; design learned; sequence design; protein ... See more keywords
Accurate prediction and key protein sequence feature identification of cyclins.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in functional genomics"
DOI: 10.1093/bfgp/elad014
Abstract: Cyclin proteins are a group of proteins that activate the cell cycle by forming complexes with cyclin-dependent kinases. Identifying cyclins correctly can provide key clues to understanding the function of cyclins. However, due to the… read more here.
Keywords: sequence features; protein sequence; cyclin; key protein ... See more keywords
Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac599
Abstract: Abstract Protein language modeling is a fast-emerging deep learning method in bioinformatics with diverse applications such as structure prediction and protein design. However, application toward estimating sequence conservation for functional site prediction has not been… read more here.
Keywords: functional sites; sequence conservation; alignment free; conservation ... See more keywords