Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.
Sign Up to like & getrecommendations! Published in 2018 at "International journal for numerical methods in biomedical engineering"
DOI: 10.1002/cnm.2914
Abstract: Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein-ligand binding affinities is… read more here.
Keywords: persistent homology; topology; protein ligand; ligand binding ... See more keywords
Structural analysis of human G‐protein‐coupled receptor 17 ligand binding sites
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Cellular Biochemistry"
DOI: 10.1002/jcb.30388
Abstract: The human G protein coupled membrane receptor (GPR17), the sensor of brain damage, is identified as a biomarker for many neurological diseases. In human brain tissue, GPR17 exist in two isoforms, long and short. While… read more here.
Keywords: ligand binding; gpr17; receptor; binding sites ... See more keywords
Benchmarking biomolecular force field‐based Zn2+ for mono‐ and bimetallic ligand binding sites
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27052
Abstract: Zn2+ is one of the most versatile biologically available metal ions, but accurate modeling of Zn2+‐containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn2+ models are parameterized in bulk solvent,… read more here.
Keywords: ligand binding; biomolecular force; zn2 models; force field ... See more keywords
The β8 integrin EGF domains support a constitutive extended conformation, and the cytoplasmic domain impairs outside‐in signaling
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Cellular Physiology"
DOI: 10.1002/jcp.30871
Abstract: Integrins are transmembrane proteins that transmit bi‐directional signals across the cell membrane through global structural rearrangement among three different conformational states: bent, extended‐ closed, and extended‐open conformations. However, the β8 integrin is distinctive and may… read more here.
Keywords: conformation; ligand binding; outside signaling; extended conformation ... See more keywords
Translating from Proteins to Ribonucleic Acids for Ligand‐binding Site Detection
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Informatics"
DOI: 10.1002/minf.202200059
Abstract: Identifying druggable ligand‐binding sites on the surface of the macromolecular targets is an important process in structure‐based drug discovery. Deep‐learning models have been shown to successfully predict ligand‐binding sites of proteins. As a step toward… read more here.
Keywords: acids ligand; ligand binding; translating proteins; ribonucleic acids ... See more keywords
More is simpler: Decomposition of ligand‐binding affinity for proteins being disordered
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4375
Abstract: In statistical mechanics, it is well known that the huge number of degrees of freedom does not complicate the problem as it seems, but actually greatly simplifies the analysis (e.g., to give a Boltzmann distribution).… read more here.
Keywords: simpler decomposition; ligand binding; binding affinity; decomposition ligand ... See more keywords
Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1154-8_12
Abstract: Protein motions play a fundamental role in enzyme catalysis and ligand binding. The relationship between protein motion and function has been extensively investigated in the model enzyme dihydrofolate reductase (DHFR). DHFR is an essential enzyme… read more here.
Keywords: protein; dihydrofolate reductase; ligand interactions; ligand binding ... See more keywords
A Ligand-Binding Assay to Measure the Affinity and Specificity of Sterol-Binding Proteins In Vitro.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7183-1_25
Abstract: Sterols are major constituents of the plasma membrane of eukaryotic cells and serve as a precursor for several classes of signaling molecules, including steroids and hydroxy sterols. They maintain the functionality and permeability barrier of… read more here.
Keywords: binding assay; specificity sterol; assay measure; measure affinity ... See more keywords
Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7465-8_17
Abstract: An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important-albeit static-pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD)… read more here.
Keywords: protein coupled; ligand binding; dynamics simulations; molecular dynamics ... See more keywords
Bcl-2 and IP3 compete for the ligand-binding domain of IP3Rs modulating Ca2+ signaling output
Sign Up to like & getrecommendations! Published in 2019 at "Cellular and Molecular Life Sciences"
DOI: 10.1007/s00018-019-03091-8
Abstract: Bcl-2 proteins have emerged as critical regulators of intracellular Ca2+ dynamics by directly targeting and inhibiting the IP3 receptor (IP3R), a major intracellular Ca2+-release channel. Here, we demonstrate that such inhibition occurs under conditions of basal,… read more here.
Keywords: bh4 domain; ligand binding; ip3; ca2 ... See more keywords
Ligand-binding and -scavenging of the chemerin receptor GPR1
Sign Up to like & getrecommendations! Published in 2021 at "Cellular and Molecular Life Sciences"
DOI: 10.1007/s00018-021-03894-8
Abstract: Graphic abstract Tight regulation of cytokines is essential for the initiation and resolution of inflammation. Chemerin, a mediator of innate immunity, mainly acts on chemokine-like receptor 1 (CMKLR1) to induce the migration of macrophages and… read more here.
Keywords: receptor gpr1; ligand binding; chemerin receptor; gpr1 ... See more keywords