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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References

SHOWING 1-10 OF 43 REFERENCES
Computational chemistry applied to the design of chiral stationary phases for enantiomeric separation
A general computational scheme for the rational design of chiral stationary phases for the chromatographic separation of enantiomers has been established. The developed scheme was based on applying
An improved molecular modeling method for the prediction of enantioselectivity
An improved method for the calculation of enantioselectivity by molecular mechanics is presented. This method does not use any a priori assumption on the conformation of the molecules in the complex
Effects of computational variations for determining binding energies of diastereomeric complexes when using MM2
Variations of a procedure have been examined for minimization of the energies, calculated using MM2, of two docked molecules. After doing the intramolecular minimization of the individual molecules,
A molecular dynamics investigation of chiral discrimination complexes as chiral stationary‐phase models: Methyl N‐(2‐naphthyl)alaninate with N‐(3,5‐dinitrobenzoyl)leucine n‐propylamide
Molecular dynamics simulations were performed on complexes of (S)-methyl N-(2-naphthyl)alaninate (NAP) with the enantiomers of N-(3,5-dinitrobenzoyl)leucine n-propylamide (DNB), which are used as
Computational chemical studies of chiral stationary‐phase models: The nature of the Pi interaction in complexes of methyl N‐(2‐naphthyl) alaninate with N‐(3,5‐dinitrobenzoyl)leucine n‐propylamide
The pi interaction in complexes of (S)-methyl N-(2-naphthyl)alaninate with (S)- and (R)-N-(3,5-dinitrobenzoyl)leucine n-propylamide was investigated with Hartree–Fock and second-order Moller–Plesset
Theoretical studies in molecular recognition: Enantioselectivity in chiral chromatography
The enantioselective binding of optical analytes on chiral stationary phases used in column chromatography is investigated with molecular modeling techniques. By rolling the analytes over the van der
Flexible ligand docking using a genetic algorithm
TLDR
The Genetic Algorithm is used to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site to explore the orientational and conformational space of a flexible ligand within an enzyme.
A general criterion for molecular recognition: implications for chiral interactions.
TLDR
It is shown how the inequality of the distance matrices of complexes of different compounds with a resolving agent under ambient experimental conditions provides for an objective, well-defined, and simple explanation for recognition of chiral compounds.
...
...