S. M. Nikitin

  • Citations Per Year
Learn More
We present a novel scoring function for docking of small molecules to protein binding sites. The scoring function is based on a combination of two main approaches used in the field, the empirical and knowledge-based approaches. To calibrate the scoring function we used an iterative procedure in which a ligand's position and its score were determined(More)
Spectrophotometric methods are used to study the binding to DNA of Actinomycin D (AMD) and its analogues: 7-nitro-AMD; 7-amino-AMD; 7-(Z-Val-Glo-NH)-AMD; 7-(AcO- . +H2-Val-Glo-NH)-AMD; 7-(AcO- . +H2-Val-Glo-Val-Glo-NH)-AMD. The binding constants are calculated from the binding isotherm of AMD and those of the AMD analogues to calf thymus DNA obtained by(More)
We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB).(More)
The cytochemical properties of a guanine-specific synthetic fluorescent analogue of actinomycin D, 7-amino-actinomycin D, have been studied in fixed and living preparations of L cells and polytene chromosomes of salivary glands ofChironomus thummi thummi andDrosophila lummei (Hackman). 7-Amino-actinomycin D has been shown to bind to DNA-containing(More)
A technique for DNA amount determination by flow cytometry based on the use of 7-amino-actinomycin D (7-amino-AMD), a fluorescent analogue of antibiotic actinomycin has been investigated, and a particular staining procedure has been developed. The procedure includes short fixation in 70% ethanol and staining for 20 min in 10(-5)M solution of 7-amino-AMD at(More)
The TDPAC technique has been applied to study the stability of n i I n complexes with NTA and DTPA in solutions with different concentrations of stable In at pH = 7. A sample of In-DTPA complexes attached to microspheres of albumin (MSA) has been measured at temperatures of 293 and 130 K. The results show that the products formed after U 1 l n -*• u l C d(More)
The possibility of use of 7-amino-actinomycin D (7aAMD)--fluorescent analog of actinomycin D--as a specific dye for DNA staining in the suspended cells was studied by means of laser flow-cytometry. The optimal conditions for staining were obtained: 7aAMD concentration 10(-5) M, pH 7, staining time 20 min, 37 degrees C, ionic strength 0.15 M Na+. In this(More)
Equilibrium and kinetic studies are reported on the binding to DNA of actinomycin D analogues containing various substituents at position 7 of the antibiotic chromophore. The binding constants are calculated from the experimental binding isotherms of actinomycin D and its analogues to calf thymus DNA. The rate constants of the association and dissociation(More)