The conformational space of diphenylamine-2,2'-dicarboxaldehyde. “Whoever reports a saying in the name of the one who said it brings redemption to the world.”
Sign Up to like & getrecommendations! Published in 2019 at "Structural Chemistry"
DOI: 10.1007/s11224-019-1291-9
Abstract: Diphenylamine-2,2'-dicarboxaldehyde (DPADA), first reported in 1961, has served as a key building block (head unit) in dicarbonyl-diamine condensations, providing a variety of pincer-style Schiff-base ligands, leading to macrocyclic metallic complexes. The present article reports a… read more here.
Keywords: global minimum; diphenylamine; dpada monohydrazone; diphenylamine dicarboxaldehyde ... See more keywords
Redefining the Protein Kinase Conformational Space with Machine Learning.
Sign Up to like & getrecommendations! Published in 2018 at "Cell chemical biology"
DOI: 10.1016/j.chembiol.2018.05.002
Abstract: Protein kinases are dynamic, adopting different conformational states that are critical for their catalytic activity. We assess a range of structural features derived from the conserved αC helix and DFG motif to define the conformational… read more here.
Keywords: kinase conformational; kinase; conformation; protein kinase ... See more keywords
Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction
Sign Up to like & getrecommendations! Published in 2018 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2018.02.003
Abstract: Computing conformations which are essential to associate structural and functional information with gene sequences, is challenging due to the high dimensionality and rugged energy surface of the protein conformational space. Consequently, the dimension of the… read more here.
Keywords: protein; feature space; space; exploration ... See more keywords
Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space.
Sign Up to like & getrecommendations! Published in 2019 at "Structure"
DOI: 10.1016/j.str.2019.03.018
Abstract: Flexibility is often a key determinant of protein function. To elucidate the link between their molecular structure and role in an organism, computational techniques such as molecular dynamics can be leveraged to characterize their conformational… read more here.
Keywords: space; molecular dynamics; coupling molecular; dynamics deep ... See more keywords
Systematic exploration of protein conformational space using a Distance Geometry approach.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.9b00215
Abstract: The optimisation approaches classically used during the determination of protein structure encounter various diffculties, specially when the size of the conformational space is large. Indeed, in such case, algorithmic convergence criteria are more difficult to… read more here.
Keywords: geometry; distance geometry; conformational space; approach ... See more keywords
Illuminating the dark conformational space of macrocycles using dominant rotors
Sign Up to like & getrecommendations! Published in 2021 at "Nature Chemistry"
DOI: 10.1038/s41557-020-00620-y
Abstract: Three-dimensional conformation is the primary determinant of molecular properties. The thermal energy available at room temperature typically equilibrates the accessible conformational states. Here, we introduce a method for isolating unique and previously understudied conformations of… read more here.
Keywords: space macrocycles; illuminating dark; using dominant; dark conformational ... See more keywords
Binding Site and Potency Prediction of Teixobactin and other Lipid II Ligands by Statistical Base Scoring of Conformational Space Maps.
Sign Up to like & getrecommendations! Published in 2018 at "Current computer-aided drug design"
DOI: 10.2174/1573409913666170927113813
Abstract: BACKGROUND Lipid II, a peptidoglycan, is a precursor in bacterial cell synthesis. It has both hydrophilic and lipophilic properties. The molecule translocates a bacterial membrane to deliver and incorporate "building blocks" from disaccharide-pentapeptide into the… read more here.
Keywords: teixobactin; potency; lipid ligands; site ... See more keywords
Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.832847
Abstract: Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD)… read more here.
Keywords: conformational space; sampling protein; four hybrid; hybrid methods ... See more keywords
Generative Topographic Mapping of the Docking Conformational Space
Sign Up to like & getrecommendations! Published in 2019 at "Molecules"
DOI: 10.3390/molecules24122269
Abstract: Following previous efforts to render the Conformational Space (CS) of flexible compounds by Generative Topographic Mapping (GTM), this polyvalent mapping technique is here adapted to the docking problem. Contact fingerprints (CF) characterize ligands from the… read more here.
Keywords: space; docking conformational; topographic mapping; mapping docking ... See more keywords
On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides
Sign Up to like & getrecommendations! Published in 2020 at "Polymers"
DOI: 10.3390/polym13010099
Abstract: Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered… read more here.
Keywords: constant molecular; use discrete; amino acids; molecular dynamics ... See more keywords