Haven't got a glue: Protein surface variation for the design of molecular glue degraders.
Sign Up to like & getrecommendations! Published in 2021 at "Cell chemical biology"
DOI: 10.1016/j.chembiol.2021.04.009
Abstract: Molecular glue degraders are small, drug-like compounds that induce interactions between an E3 ubiquitin ligase and a target, which result in ubiquitination and subsequent degradation of the recruited protein. In recent years, serendipitous discoveries revealed… read more here.
Keywords: molecular glue; glue degraders; protein surface;
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics
Sign Up to like & getrecommendations! Published in 2018 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.7b00268
Abstract: Water molecules are an important factor in protein-ligand binding. Upon binding of a ligand with a protein's surface, waters can either be displaced by the ligand or may be conserved and possibly bridge interactions between… read more here.
Keywords: mixed solvent; water; protein surface; displaceable water ... See more keywords
Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.9b00474
Abstract: Predicting the assembly of multiple proteins into specific complexes is critical to understanding their biological function in an organism and thus the design of drugs to address their malfunction. Proteins are flexible molecules, which inherently… read more here.
Keywords: protein; protein docking; electrostatics; protein surface ... See more keywords
High affinity protein surface binding through co-engineering of nanoparticles and proteins.
Sign Up to like & getrecommendations! Published in 2022 at "Nanoscale"
DOI: 10.1039/d1nr07497k
Abstract: Control over supramolecular recognition between proteins and nanoparticles (NPs) is of fundamental importance in therapeutic applications and sensor development. Most NP-protein binding approaches use 'tags' such as biotin or His-tags to provide high affinity; protein… read more here.
Keywords: engineering nanoparticles; high affinity; affinity; protein surface ... See more keywords
Biomimetic fusion: Platyper's dual vision for predicting protein-surface interactions.
Sign Up to like & getrecommendations! Published in 2024 at "Materials horizons"
DOI: 10.1039/d4mh00066h
Abstract: Predicting protein binding with the material surface still remains a challenge. Here, a novel approach, platypus dual perception neural network (Platyper), was developed to describe the interactions in protein-surface systems involving bioceramics with BMPs. The… read more here.
Keywords: surface interactions; predicting protein; dual vision; protein surface ... See more keywords
Probing protein surface interactions in nanoaperture optical tweezers
Sign Up to like & getrecommendations! Published in 2025 at "Nanotechnology"
DOI: 10.1088/1361-6528/ae1c48
Abstract: Nanoaperture optical tweezers (NOTs) can trap single proteins using local electromagnetic field enhancements at metal surfaces and therefore they are also subject to surface interactions. To probe these interactions, we consider the power dependence of… read more here.
Keywords: surface interactions; nanoaperture optical; protein surface; surface ... See more keywords
GLYCO: a tool to quantify glycan shielding of glycosylated proteins
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab791
Abstract: MOTIVATION Glycans play important roles in protein folding and cell-cell interactions-and, furthermore, glycosylation of protein antigens can dramatically impact immune responses. While there have been attempts to quantify the glycan shielding or coverage of a… read more here.
Keywords: glycan shielding; shielding glycosylated; quantify glycan; protein surface ... See more keywords
Histone protein surface accessibility dictates direction of RSC-dependent nucleosome mobilization
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac790
Abstract: Abstract Chromatin remodeling enzymes use energy derived from ATP hydrolysis to mobilize nucleosomes and alter their structure to facilitate DNA access. The Remodels the Structure of Chromatin (RSC) complex has been extensively studied, yet aspects… read more here.
Keywords: dna; protein surface; nucleosome mobilization; rsc ... See more keywords
GeoBind: segmentation of nucleic acid binding interface on protein surface with geometric deep learning.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad288
Abstract: Unveiling the nucleic acid binding sites of a protein helps reveal its regulatory functions in vivo. Current methods encode protein sites from the handcrafted features of their local neighbors and recognize them via a classification,… read more here.
Keywords: protein surface; acid binding; geobind; deep learning ... See more keywords