A “quasi‐flexible” automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation

@article{Alcaro2000AA,
  title={A “quasi‐flexible” automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation},
  author={Stefano Alcaro and Francesco Gasparrini and Ottaviano Incani and S. Mecucci and D. Misiti and Marco Pierini and Claudio Villani},
  journal={Journal of Computational Chemistry},
  year={2000},
  volume={21}
}
The main purpose of this work is the development and validation of a general scheme based on a systematic and automatic “quasi‐flexible” docking approach for studying stereoselective recognition mechanisms. To achieve our goals we explore the conformational and configurational space for small‐ or medium‐size flexible molecules in a systematic way, seeking a method that is both reasonably accurate and relatively fast from the computational point of view. In particular, we have developed a… 
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51 Citations
Methods Citations
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51 Citations

“Quasi flexible” automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of ΔΔG of complexation and 1H‐NMR NOE correlation
TLDR
A remarkable correlation between the theoretical results and experimental data supports the validity of the computational approach and underline the importance of the conformational multiplicity in the definition of the macroscopic properties of the complex in solution.
Recent studies of docking and molecular dynamics simulation for liquid‐phase enantioseparations
TLDR
Topics and trends in using docking and molecular dynamics as theoretical complement of experimental LC and CE chiral separations are described herein and the basic concepts of these computational strategies and seminal studies performed over time are presented.
NMR and Computational Investigations of the Chiral Discrimination Processes Involving a Cyclic Tetraamidic Chiral Selector
The chiral recognition mechanism of a macrocyclic tetraamidic receptor for the enantiomers of N-(3,5-dinitrobenzoyl)valine-N-hexylamide has been investigated in detail through a combination of NMR…
Computational studies in enantioselective liquid chromatography: Forty years of evolution in docking- and molecular dynamics-based simulations
Docking experiments showing similar recognition patterns of paclitaxel when interacting with different macromolecular targets.
Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors.
Rational Design, Synthesis, Biophysical and Antiproliferative Evaluation of Fluorenone Derivatives with DNA G‐Quadruplex Binding Properties
TLDR
Results of theoretical, biophysical, and in vitro experiments indicate two novel derivatives as lead compounds for the development of a new generation of G‐quadruplex ligands with greater potency and selectivity.
Encoding Absolute Configurations with Chiral Enantiophore Descriptors. Application to the Order of Elution of Enantiomers in Liquid Chromatography
New chiral descriptors based on pharmacophore perception around the chiral center are used for the prediction of the orders of elution in chiral chromatography and are associated to the absolute…
Computer-Aided Molecular Design of Asymmetric Pyrazole Derivatives with Exceptional Enantioselective Recognition toward the Chiralcel OJ-H Stationary Phase
TLDR
Looking at the time spent by each enantiomer in contact with the CSP during long molecular dynamic simulations, the experimental analytical trend has been reproduced and the theoretical prediction of the enantioselective recognition process was confirmed.
Analysis of chiral chromatographic separations by molecular modeling
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