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Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond
Cyclic peptides formed by disulfide bonds have been one large group of common drug candidates in drug development. Structural information of a...
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Interplay Between Conformation and Hydrogen Bond Pattern: Crystal Structure of N-(2,2-dichloroacetyl)-N',N"-dipropylphosphoric Triamide and a Database Survey
The interplay between conformation and hydrogen bond pattern was studied in 211 (C(O)NH)(N) 2 P(O)-based phosphoric triamides retrieved from the...
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Adsorption of Glycerol at Brønsted Sites in Mordenite: a Density Functional Theory Study
AbstractAdsorption of various glycerol conformations at Brønsted sites in mordenite is studied by the density functional theory. It is shown that the...
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Aromaticity of Cope and Claisen rearrangements
Claisen and Cope rearrangements are [3,3]-sigmatropic rearrangements thermally activated that occur through six-membered transition states. Although...
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Biostatistical Investigation Using Docking Mechanism and Its Database to Investigate Drug Design, Drug Discovery, Drug Metabolism and Prediction Via Drug–Drug Interactions
Molecular docking is an important tool for structure-based drug design and is being widely used to study molecular interactions with proteins at...
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Prediction of Peptide and TCR CDR3 Loops in Formation of Class I MHC-Peptide-TCR Complexes Using Molecular Models with Solvation
Formation of major histocompatibility (MHC)-peptide-T cell receptor (TCR) complexes is central to initiation of an adaptive immune response. These...
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Effects of intramolecular hydrogen bonding on nuclear magnetic resonance, electron paramagnetic resonance and molecular docking studies: Mexiletine molecule
ContextIn this study, the molecular structure of the mexiletine molecule was investigated. Since the Mexiletine molecule is a drug active ingredient,...
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Physics-Based Polymer Models to Probe Chromosome Structure in Single Molecules
Human chromosomes have a complex 3D spatial organization in the cell nucleus, which comprises a hierarchy of physical interactions across genomic...
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Study of the Role of Conformation of Thiophene Oligomers on Their Electronic and Magnetic Properties
AbstractCorrelations of electronic and magnetic resonance parameters of spin charge carriers in thiophene oligomers with their polymerization degrees...
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Conformational tuning improves the stability of spirocyclic nitroxides with long paramagnetic relaxation times
Nitroxides are widely used as probes and polarization transfer agents in spectroscopy and imaging. These applications require high stability towards...
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Role of Conformational Entropy in Complex Macromolecular Systems
C onformation is the key to revealing the physical characteristics of macromolecular systems and receives tremendous interest from the fields of...
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“Chair”–“Boat” Conformational Transition of Cyclohexanone during the Oxidation of Cyclohexane
AbstractThe B3LYP/6-311g++( d , p ), G3, and CBS-QB3 methods (DFT) have been used to calculate the free energy and equilibrium constants of the...
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Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides
Gas-phase conformations of the sodium-cationized forms of the 2′-deoxycytidine and cytidine mononucleotides, [pdCyd+Na] + and [pCyd+Na] + , are examined...
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Production and Purification of Hantavirus Glycoproteins in Drosophila melanogaster S2 Cells
Hantaviruses, are rodent-borne viruses found worldwide that are transmitted to humans through inhalation of contaminated excreta. They can cause a...
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Modeling Conformational Rearrangements of a Macromolecule Adsorbed on a Metal Nanoparticle in an External Electric Field
AbstractThe properties of a specially created analytical model of conformational rearrangements of a Gaussian macromolecular chain adsorbed on the...
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Determining Conformations and Sizes of Polyethylene Glycol Macromolecules in Water–Polyethylene Glycol–LiOH Systems by the Viscometry Method
The kinematical viscosity of water-polyethylene glycol-LiOH systems is studied at 293.15 K for the LiOH molar fraction of 0–0.05 and the PEG...
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Deciphering the conformational transitions of LIMK2 active and inactive states to ponder specific druggable states through microsecond scale molecular dynamics simulation
LIMK2 inhibitors are one of the potential therapeutic modalities for treating various diseases. In the current scenario, there is a paucity of...
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Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing
The group I self-splicing introns, like other RNAs and RNA–protein complexes, undergo multiple conformational changes in completing two...
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Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators
Fragment-based drug discovery is an established methodology for finding hit molecules that can be elaborated into lead compounds. However it is...
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DFT study of the conformation, hydrogen bonds, IR, Raman, and NMR spectra of 1,3-disubstituted p-tert-butylthiacalix[4]arenes
ContextThe molecular design of spatially preorganized molecules is one of the critical issues in organic chemistry. Molecular recognition and...
