• Journal of Integrative Natural Science
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• v.2 no.2
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• pp.55-58
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• 2009

A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Bulletin of the Korean Chemical Society
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• v.24 no.1
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• pp.75-80
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• 2003

The structures and complexation energies of penta-O-alkylated 1b and penta-O-tert-butyl ester 1e of p-tert-butylcalix[5]arene and their simplified structures (2b and 2e) toward a series of alkyl ammonium guests have been calculated by a semi-empirical AM1 method. For AM1 calculations, complexation efficiencies of the simplified host 2e are very similar to the values of host 1e. The complexes of simplified host 2e with alkyl ammonium ions also have been optimized by ab initio HF/6-31G method. The calculated complexation efficiencies for 2e by ab initio method have been found to be bigger in magnitude than the values obtained by AM1 calculations for linear alkyl ammonium guests. Calculation results show that all of the calix[5]aryl derivatives investigated in this study have much better complexation ability toward ammonium cation without alkyl group compared with other alkyl ammonium guests. Ab initio calculations also well duplicate the molecular discriminating behaviors of calix[5]arene derivative 2e between butyl ammonium ions: $n-BuNH_3^+\;>\;iso-BuNH_3^+\;>\;sec-BuNH_3^+\;>\;tert-BuNH_3^+$.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4215-4220
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• 2012

AML (Acute myeloid leukemia) is a form of blood cancer where growth of myeloid cells occurs in the bone marrow. The prognosis is poor in general for many reasons. One is the presence of leukaemia-specific recognition markers such as FLT3 (fms-like tyrosine kinase 3). Another name of FLT3 is stem cell tyrosine kinase-1 (STK1), which is known to take part in proliferation, differentiation and apoptosis of hematopoietic cells, usually being present on haemopoietic progenitor cells in the bone marrow. FLT3 act as an independent prognostic factor for AML. Although a vast literature is available about the association of FLT3 with AML there still is a need of a brief up to date overview which draw a clear picture about this association and their effect on overall survival.

• BMB Reports
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• v.39 no.3
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• pp.263-269
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• 2006

In the genome of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus, open reading frame 39 (Ha39) is the only gene predicted to encode an RNA recognition protein. Computer analysis revealed that Ha39 homologues were found in 15 NPVs, but not in GVs. Its transcripts were detected from 3 through 72 hours post infection (h p.i.) using RT-PCR and Northern blot analysis. The protein was detected in infected-cell lysates from 6 h p.i. Western blot assay of ODV and BV preparations revealed that Ha39 encodes a structural protein associated with BVs. Additionally, immunofluorescence microscopy demonstrated that the protein was present within cytoplasm in virus-infected cells, but not in the nuclear region.

• Bulletin of the Korean Chemical Society
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• v.28 no.8
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• pp.1346-1352
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• 2007

This article presents an original work on kinetically studying the selective adsorption and recognition by molecularly imprinted polymer (MIP). With S-naproxen as template, the imprinted polymer was prepared. The result indicates that the prepared polymer shows a more complicated sorption toward S-naproxen than toward its enantiomer R-naproxen. The rate constant in the case of template appears to be a variable. There are also significant deviations from the idealized Langmuir model. Related information indicates that these, in logic, can be a result of biomimic structural and functional complements between imprint and the template, which makes the polymer capable of selectively recognizing the imprint species.

• Communications of the Korean Institute of Information Scientists and Engineers
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• v.18 no.8
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• pp.78-89
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• 2000

Today's computers are built up from a minimal set of standard pattern recognition operations. Logic gates, such as NAND, are common examples. Biomolecular materials offer an alternative approach, both in terms of variety and context sensitivity. Enzymes, the basic switching elements in biological cells, are notable for their ability to discriminate specific molecules in a complex background and to do so in a manner that is sensitive to particular milieu features and indifferent to others, The enzyme, in effect, is a powerful context sensitivity pattern processor that in a rough way can be analogized to a neuron whose input-output behavior is controlled by enzymatic dynamics.

• Molecules and Cells
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• v.39 no.5
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• pp.375-381
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• 2016

MicroRNAs (miRNAs) are small non-coding RNAs (~22 nucleotides) regulating gene expression at the post-transcriptional level. By directing the RNA-induced silencing complex (RISC) to bind specific target mRNAs, miRNA can repress target genes and affect various biological phenotypes. Functional miRNA target recognition is known to majorly attribute specificity to consecutive pairing with seed region (position 2-8) of miRNA. Recent advances in a transcriptome-wide method of mapping miRNA binding sites (Ago HITS-CLIP) elucidated that a large portion of miRNA-target interactions in vivo are mediated not only through the canonical "seed sites" but also via non-canonical sites (~15-80%), setting the stage to expand and determine their properties. Here we focus on recent findings from transcriptome-wide non-canonical miRNA-target interactions, specifically regarding "nucleation bulges" and "seed-like motifs". We also discuss insights from Ago HITS-CLIP data alongside structural and biochemical studies, which highlight putative mechanisms of miRNA target recognition, and the biological significance of these non-canonical sites mediating marginal repression.

• Molecules and Cells
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• v.27 no.6
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• pp.681-687
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• 2009

We examined the effects of synthetic signal peptides, wild-type (WT) and export-defective mutant (MT) of ribose-binding protein, on the conformational changes of signal recognition particle 54 homologue (Ffh) in Escherichia coli. Upon interaction of Ffh with WT peptide, the intrinsic Tyr fluorescence, the transition temperature of thermal unfolding, and the GTPase activity of Ffh decreased in a peptide concentration-dependent manner, while the emission intensity of 8-anilinonaphthalene-1-sulfonic acid increased. In contrast, the secondary structure of the protein was not affected. Additionally, polarization of fluorescein-labeled WT increased upon association with Ffh. These results suggest that WT peptide induces the unfolded states of Ffh. The WT-mediated conformational change of Ffh was also revealed to be important in the interaction between SecA and Ffh. However, MT had marginal effect on these conformational changes suggesting that the in vivo functionality of signal peptide is important in the interaction with Ffh and concomitant structural change of the protein.

• Polymer(Korea)
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• v.37 no.3
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• pp.288-293
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• 2013

A group of molecularly imprinted polymers (MIPs) with specific recognition for chiral (S)-ibuprofen were successfully prepared based on hydrogen bonds, utilizing ${\alpha}$-methacrylic acid as a functional monomer. The IR analysis of MIPs showed that the blue- and red-shifted hydrogen bonds were formed between templates and functional monomers in the process of self-assembly imprinting and re-recognition, respectively. According to UV-Vis analysis, we found that the ratio of host-guest complexes between template molecule and functional monomer was 1:1. The effect of cross-linker's quantity on the polymerization was studied by transmission electron microscope (TEM). The adsorption selectivity experiments indicated that MIPs exhibited higher selectivity to (S)-ibuprofen than those to ketoprofen and (R)-ibuprofen, (S)-ibuprofen's structural analogs.