The Usage of ACCLUSTER for Peptide Binding Site Prediction.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-6798-8_1
Abstract: Peptides mediate up to 40 % of protein-protein interactions in a variety of cellular processes and are also attractive drug candidates. Thus, predicting peptide binding sites on the given protein structure is of great importance… read more here.
Keywords: peptide binding; accluster; accluster peptide; binding site ... See more keywords
Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles
Sign Up to like & getrecommendations! Published in 2020 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2019.107195
Abstract: Major Histocompatibility Complex (MHC) is a cell surface glycoprotein that binds to foreign antigens and presents them to T lymphocyte cells on the surface of Antigen Presenting Cells (APCs) for appropriate immune recognition. Recently, studies… read more here.
Keywords: peptide binding; investigation peptide; binding stabilities; hla ... See more keywords
Molecular mechanisms of plant peptide binding to receptors
Sign Up to like & getrecommendations! Published in 2021 at "Peptides"
DOI: 10.1016/j.peptides.2021.170614
Abstract: Plants have evolved diverse peptide hormones and cognate receptors to orchestrate plant growth and development. Secreted peptide ligands are mainly sensed by membrane receptor kinases that mediate cell-cell communication. The secreted peptides are categorized into… read more here.
Keywords: peptide binding; mechanisms plant; plant; molecular mechanisms ... See more keywords
An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00583
Abstract: The prediction of peptide-protein binding sites is of utmost importance to tackle the onset of severe neurodegenerative diseases and cancer. In this work, we detail a novel machine learning model based on Linear Discriminant Analysis… read more here.
Keywords: learning model; peptide binding; machine learning; pockets protein ... See more keywords
Accurate Prediction for Protein-Peptide Binding Based on High-Temperature Molecular Dynamics Simulations.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00743
Abstract: The structural characterization of protein-peptide interactions is fundamental to elucidating biological processes and designing peptide drugs. Molecular dynamics (MD) simulations are extensively used to study biomolecular systems. However, simulating the protein-peptide binding process is usually… read more here.
Keywords: dynamics simulations; protein peptide; peptide binding; molecular dynamics ... See more keywords
Lysine Acetylation Changes the Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer.
Sign Up to like & getrecommendations! Published in 2023 at "ACS chemical neuroscience"
DOI: 10.1021/acschemneuro.2c00722
Abstract: The impact of Lys28 acetylation on Alzheimer's Aβ peptide binding to the lipid bilayer has not been previously studied, either experimentally or computationally. To probe this common post-translational modification, we performed all-atom replica exchange molecular… read more here.
Keywords: acetylation; aggregation; dmpc bilayer; bilayer ... See more keywords
Harnessing Peptide Binding to Capture and Reclaim Phosphate.
Sign Up to like & getrecommendations! Published in 2021 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.1c01241
Abstract: With rising consumer demands, society is tapping into wastewater as an innovative source to recycle depleting resources. Novel reclamation technologies have been recently explored for this purpose, including several that optimize natural biological processes for… read more here.
Keywords: peptide binding; harnessing peptide; reclaim phosphate; capture ... See more keywords
Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-18204-2
Abstract: CD4+ helper T cells contribute important functions to the immune response during pathogen infection and tumor formation by recognizing antigenic peptides presented by class II major histocompatibility complexes (MHC-II). While many computational algorithms for predicting… read more here.
Keywords: peptide binding; yeast display; prediction; mhc ... See more keywords
Significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium
Sign Up to like & getrecommendations! Published in 2022 at "RSC Advances"
DOI: 10.1039/d2ra00535b
Abstract: We selected the G-quadruplex motif located in the nuclease-hypersensitive elements (NHE) III1 region of the c-Myc promoter and for the first time performed its interaction studies with a designed peptide (QW10). Our CD results showed… read more here.
Keywords: peptide binding; myc promoter; significant structural; myc ... See more keywords
Predicting protein-peptide binding residues via interpretable deep learning
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac352
Abstract: AVAILABILITY Identifying the protein-peptide binding residues is fundamentally important to understand the mechanisms of protein functions and explore drug discovery. Although several computational methods have been developed, they highly rely on third-party tools or information… read more here.
Keywords: protein peptide; peptide binding; pepbcl; deep learning ... See more keywords
PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity
Sign Up to like & getrecommendations! Published in 2017 at "GigaScience"
DOI: 10.1093/gigascience/gix017
Abstract: Abstract Predicting peptide binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA… read more here.
Keywords: peptide binding; class; pssmhcpan; hla ... See more keywords