Revealing protein structures: crystallization of protein‐ligand complexes – co‐crystallization and crystal soaking
Sign Up to like & getrecommendations! Published in 2024 at "FEBS Open Bio"
DOI: 10.1002/2211-5463.13913
Abstract: Protein crystallogenesis represents a key step in X‐ray crystallography studies that employ co‐crystallization and ligand soaking for investigating ligand binding to proteins. Co‐crystallization is a method that enables the precise determination of binding positions, although… read more here.
Keywords: revealing protein; crystallization; protein structures; protein ligand ... See more keywords
Intelligent molecular orientation transformation in 3D printing system
Sign Up to like & getrecommendations! Published in 2018 at "Microsystem Technologies"
DOI: 10.1007/s00542-017-3289-9
Abstract: Proper orientation of a molecular structure in three-dimensional (3D) printing could increase successful printing rates, reduce the amount of supporting material required, and shorten printing time. In traditional approaches, manual adjustment of a target object… read more here.
Keywords: intelligent molecular; molecular orientation; protein structures; orientation ... See more keywords
Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures
Sign Up to like & getrecommendations! Published in 2019 at "Amino Acids"
DOI: 10.1007/s00726-019-02743-0
Abstract: Extracting a well-designed energy function is important for protein structure evaluation. Knowledge-based potential functions are one type of the energy functions which can be obtained from known protein structures. The pairwise potential between atom types… read more here.
Keywords: protein structures; amino; amino acids; energy ... See more keywords
Hydrophobic interactions of sucralose with protein structures.
Sign Up to like & getrecommendations! Published in 2018 at "Archives of biochemistry and biophysics"
DOI: 10.1016/j.abb.2017.12.013
Abstract: Sucralose is a commonly employed artificial sweetener that appears to destabilize protein native structures. This is in direct contrast to the bio-preservative nature of its natural counterpart, sucrose, which enhances the stability of biomolecules against… read more here.
Keywords: state; sucralose protein; protein structures; hydrophobic interactions ... See more keywords
Evaluation of variability in high-resolution protein structures by global distance scoring
Sign Up to like & getrecommendations! Published in 2018 at "Heliyon"
DOI: 10.1016/j.heliyon.2018.e00510
Abstract: Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details… read more here.
Keywords: resolution; high resolution; protein structures; distance scoring ... See more keywords
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry.
Sign Up to like & getrecommendations! Published in 2020 at "Structure"
DOI: 10.1016/j.str.2020.08.005
Abstract: Ramachandran plots report the distribution of the (ϕ, ψ) torsion angles of the protein backbone and are one of the best quality metrics of experimental structure models. Typically, validation software reports the number of residues… read more here.
Keywords: protein structures; ramachandran score; identifies protein; score identifies ... See more keywords
Quantitative Structural Proteomics Unveils the Conformational Changes of Proteins under the Endoplasmic Reticulum Stress.
Sign Up to like & getrecommendations! Published in 2022 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.2c03076
Abstract: Protein structures are decisive for their activities and interactions with other molecules. Global analysis of protein structures and conformational changes cannot be achieved by commonly used abundance-based proteomics. Here, we integrated cysteine covalent labeling, selective… read more here.
Keywords: endoplasmic reticulum; protein structures; reticulum stress; conformational changes ... See more keywords
Assessing AlphaFold 3 for Per- and Polyfluoroalkyl Substances Docking in Protein Structures
Sign Up to like & getrecommendations! Published in 2025 at "Environmental Science & Technology"
DOI: 10.1021/acs.est.5c03917
Abstract: Per- and polyfluoroalkyl substances (PFAS) are persistent environmental pollutants that may pose health risks due to strong protein interactions. While AlphaFold 3 (AF3) was recently introduced for protein–ligand modeling with high claimed accuracy, its reliability… read more here.
Keywords: pfas; protein structures; per polyfluoroalkyl; protein ... See more keywords
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00436
Abstract: Macrocycles are interesting molecules with unique features due to their conformationally constrained yet flexible ring structure. This characteristic poses a difficult challenge for computational modeling studies since they rely on accurate structural descriptions. In particular,… read more here.
Keywords: unbound protein; protein structures; bound unbound; dynamic docking ... See more keywords
Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00885
Abstract: The structure of a protein is of great importance in determining its functionality, and this characteristic can be leveraged to train data-driven prediction models. However, the limited number of available protein structures severely limits the… read more here.
Keywords: protein structures; predicted structures; function prediction; alphafold predicted ... See more keywords
Light-Induced Printing of Protein Structures on Membranes in Vitro.
Sign Up to like & getrecommendations! Published in 2018 at "Nano letters"
DOI: 10.1021/acs.nanolett.8b03187
Abstract: Reconstituting functional modules of biological systems in vitro is an important yet challenging goal of bottom-up synthetic biology, in particular with respect to their precise spatiotemporal regulation. One of the most desirable external control parameters… read more here.
Keywords: protein; protein structures; printing protein; light induced ... See more keywords