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
In Silico Fold-Switching Protein Design Driven by Cα-Based Statistical Potential
Sign Up to like & getrecommendations! Published in 2025 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.5c01435
Abstract: Structural plasticity of naturally occurring proteins allows them to change their shape in response to environmental factors such as pH, temperature, or binding partners. This ability to adopt different conformations is essential for many biological… read more here.
Keywords: sequence similarity; design; protein sequences; fold switching ... See more keywords
Phylogenetically informative proteins from an Early Miocene rhinocerotid
Sign Up to like & getrecommendations! Published in 2025 at "Nature"
DOI: 10.1038/s41586-025-09231-4
Abstract: In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference1, 2, 3–4. Still, even though ancient proteins have been reported from the Middle–Late Miocene5,6, the recovery… read more here.
Keywords: informative proteins; early miocene; rhinocerotid; protein sequences ... See more keywords
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures
Sign Up to like & getrecommendations! Published in 2024 at "Nature Methods"
DOI: 10.1038/s41592-024-02409-0
Abstract: Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link… read more here.
Keywords: genomics proteins; discovery tool; protein sequences; proteins portal ... See more keywords
MMV method: a new approach to compare protein sequences under binary representation
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Biomolecular Structure and Dynamics"
DOI: 10.1080/07391102.2024.2317982
Abstract: Abstract In the present work, a new form of descriptor using minimal moment vector (MMV) is introduced to compare protein sequences in the frequency domain under their component wise binary representations. From every sequence, 20… read more here.
Keywords: protein sequences; mmv method; method new; compare protein ... See more keywords