Search results for "molecular modeling"
showing 6 items of 136 documents
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
2019
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics‐generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Noble Gases as Magnetic Probes in Fullerene Chemistry
2016
Since the early 1990s of the previous century, the use of magnetic active noble gas atom to indirectly probe the size and symmetry of fullerene cage has been reviewed. Molecular modeling of nuclear shielding (and chemical shift) using gauge-including atomic orbital (GIAO) approach at several levels of theory, including Hartree–Fock (HF), density functional theory (DFT), and coupled cluster (CC), is discussed. The advantage of using GIAO calculation to predict and closely reproduce experimental 3He and 129Xe NMR spectra is shown.
Synthesis of Hybrid Tripeptide Peptidomimetics Containing Dehydroamino Acid and Aminophosphonic Acid in the Chain and Evaluation of Their Activity to…
2021
Synthesis of a new group of hybrid phosphonodehydropeptides composed of glycyl-(Z)-dehydrophenylalanine and structurally variable aminophosphonates alongside with investigations of their activity towards cathepsin C are presented. Obtained results suggest that the introduction of (Z)- dehydrophenylalanine residue into the short phosphonopeptide chain does induce the ordered conformation. Investigated peptides appeared to act as weak or moderate inhibitors of cathepsin C.
Applications of Quantum Chemistry in Spectroscopy: Molecules, Complexes of Van der Waals, trapped Molecules
2009
I described in this memory my activities as a researcher at Tomsk well before 2003, in succession to the State University of Tomsk in the Faculty of Physics, Institute of Physics of Siberia, and the Institute of 'Atmospheric Optics, in France since then, mostly at the University of Bourgogne (ICB), but also at the University of Lille I (PhLAM) and the University of Marne-la-Vallée (LCT). Part of my work has been dedicated to the evaluation by calculating ab initio of rovibrational constants for quasi-spherical molecules. The centrifugal distortion constants and the dipole moment of the molecule SO2F2 were calculated to validate the tensor theory and interpreter the spectrum. I twas shown th…
Understanding the Interactions of Guanine Quadruplexes with Peptides as Novel Strategies for Diagnosis or Tuning Biological Functions
2023
Guanine quadruplexes (G4s) are nucleic acid structures exhibiting a complex structural behavior and exerting crucial biological functions, in both cells and viruses. The specific interactions of peptides with G4s, as well as the understanding of the factors driving the specific recognition, are important for the rational design of both therapeutic and diagnostic agents. In the present minireview, we examine the most important studies dealing with the interactions between G4s and peptides, highlighting the strengths and limitations of the present analytic approaches. We also show how the combined use of high-level molecular simulation techniques and experimental spectroscopy represents the b…
Classical and reverse substituent effects in meta- and para-substituted nitrobenzene derivatives
2017
Electron-accepting properties of the nitro group were studied in a series of meta- and para-X-substituted nitrobenzene derivatives (X = NMe2, NH2, OH, OMe, CH3, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, COCl, NO2, NO). For this purpose Hammett-like approaches were applied based on quantum chemistry modeling; the B3LYP/6-311++ G(d,p) method was used. The substituent effect (SE) was characterized by the mutually interrelated descriptors: the charge of the substituent active region, cSAR(X), and substituent effect stabilization energy, SESE, as well as substituent constants, σ. Classical SE is realized by dependences of the structural parameters of the nitro group (ONO angle and NO bond lengt…