A novel numerical model for protein sequences analysis based on spherical coordinates and multiple physicochemical properties of amino acids.
Sign Up to like & getrecommendations! Published in 2019 at "Biopolymers"
DOI: 10.1002/bip.23282
Abstract: How to characterize short protein sequences to make an effective connection to their functions is an unsolved problem. Here we propose to map the physicochemical properties of each amino acid onto unit spheres so that… read more here.
Keywords: physicochemical properties; numerical model; protein sequences; properties amino ... See more keywords
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
PANTHER: Making genome‐scale phylogenetics accessible to all
Sign Up to like & getrecommendations! Published in 2021 at "Protein Science"
DOI: 10.1002/pro.4218
Abstract: Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their evolutionary relationships to other proteins. However, phylogenetics analyses can be challenging: they are computationally expensive and must be performed carefully in order to… read more here.
Keywords: making genome; panther making; scale phylogenetics; genome scale ... See more keywords
FLAVI: An Amino Acid Substitution Model for Flaviviruses
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Molecular Evolution"
DOI: 10.1007/s00239-020-09943-3
Abstract: Amino acid substitution models represent substitution rates among amino acids during the evolution. The models play an important role in analyzing protein sequences, especially inferring phylogenies. The rapid evolution of flaviviruses is expanding the threat… read more here.
Keywords: amino acid; substitution model; model; protein sequences ... See more keywords
Multi-label classifier for protein sequence using heuristic-based deep convolution neural network
Sign Up to like & getrecommendations! Published in 2021 at "Applied Intelligence"
DOI: 10.1007/s10489-021-02529-6
Abstract: Deep learning techniques are found very useful to classify sequential data in recent times. The protein sequences belong to the functional classes based on the structure of their sequences. The annotation task of protein sequences… read more here.
Keywords: protein; multi label; functional classes; protein sequences ... See more keywords
DNA Motif Recognition Modeling from Protein Sequences
Sign Up to like & getrecommendations! Published in 2018 at "iScience"
DOI: 10.1016/j.isci.2018.09.003
Abstract: Summary Although the existing works on DNA motif discovery on DNA sequences are plethoric, mechanistic knowledge to infer DNA motifs from protein sequences across multiple DNA-binding domain families without conducting any wet-lab experiments is still… read more here.
Keywords: dna; motif recognition; protein sequences; recognition modeling ... See more keywords
Extracting features from protein sequences to improve deep extreme learning machine for protein fold recognition.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2017.03.023
Abstract: Protein fold recognition is an important problem in bioinformatics to predict three-dimensional structure of a protein. One of the most challenging tasks in protein fold recognition problem is the extraction of efficient features from the… read more here.
Keywords: features protein; protein fold; protein sequences; fold recognition ... See more keywords
DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences.
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab336
Abstract: Efforts to elucidate protein-DNA interactions at the molecular level rely in part on accurate predictions of DNA-binding residues in protein sequences. While there are over a dozen computational predictors of the DNA-binding residues, they are… read more here.
Keywords: binding residues; dna; dna type; protein sequences ... See more keywords
DeepSF: deep convolutional neural network for mapping protein sequences to folds
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx780
Abstract: Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of… read more here.
Keywords: protein; protein sequences; fold recognition; neural network ... See more keywords
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac252
Abstract: pH regulates protein function and interactions by altering the charge of individual residues causing the loss or gain of intra-molecular non-covalent bonds, which may additionally lead to structural rearrangements. While tools to analyze residue-specific charge… read more here.
Keywords: sensitivity analysis; protein sequences; non covalent; sequences structures ... See more keywords
A Novel Image Cryptosystem Inspired by the Generation of Biological Protein Sequences
Sign Up to like & getrecommendations! Published in 2023 at "IEEE Access"
DOI: 10.1109/access.2023.3261133
Abstract: Image encryption is essential to keep images secure either in personal devices or over the cloud drives. Various robust image cryptosystems have been implemented during the past decades to keep the encrypted images far from… read more here.
Keywords: novel image; protein sequences; cryptosystem; image cryptosystem ... See more keywords