• Journal of the Korean Chemical Society
• /
• v.55 no.5
• /
• pp.733-740
• /
• 2011

Multiple regression analysis was used for the calculation of pKa values of 15 substituted benzaldoximes by using various types of descriptors as parameters. These descriptors are based on quantum mechanical treatments. They were derived by employing semi-empirical calculation represented by the PM3 model and an Abinitio method expressed by Hartree-Fock(HF) model performed at the 6-311 G(d, p) level of theory. The parameters tested for their ability to represent the variations observed in the experimental pKa(s) are atomic and structural properties including Muliken charges on the atoms of hydroxyl group and C=N bond, the angle $C_6-C_1-C_7$, and length of O-H bond. Molecular properties are also used like energies of HOMO and LUMO, hardness(${\eta}$), chemical potential(${\mu}$), total energy(TE), dipole of molecule(DM), and electrophilicity index(W). The relation between pKa values and each of these parameters of the studied compounds is investigated. Depending on these relations, two sets of parameters were constructed for comparison between the PM3 and HF methods. The results obtained favor the Abinitio method for such applications although both models proved to have high predictive power and have sufficient reliability to describe the effect of substituents on pKa values of benzaldoxime compounds under consideration which is clear from the values of correlation coefficient $R^2$ obtained and the consistency between the experimental and the calculated values.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.3
• /
• pp.837-850
• /
• 2013

Bovine viral diarrhea virus (BVDV), a major pathogen of cattle, is a well-characterized pestivirus which has been used as a good model virus for HCV. The RNA-dependent RNA polymerase (RdRp) plays a key role in the RNA replication process, thus it has been targeted for antivirus drugs. We employed two-dimensional quantitative structure-activity relationship (2D-QSAR) and molecular field analysis (MFA) to identify the molecular substructure requirements, and the particular characteristics resulted in increased inhibitory activity for the known series of compounds to act as effective BVDV inhibitors. The 2D-QSAR study provided the rationale concept for changes in the structure to have more potent analogs focused on the class of arylazoenamines, benzimidazoles, and acridine derivatives with an optimal subset of descriptors, which have significantly contributed to overall anti-BVDV activity. MFA represented the molecular patterns responsible for the actions of antiviral compound at their receptors. We conclude that the polarity and the polarizability of a molecule play a main role in the inhibitory activity of BVDV inhibitors in the QSAR modeling.

• Bulletin of the Korean Chemical Society
• /
• v.29 no.3
• /
• pp.647-655
• /
• 2008

Microsomal prostaglandin E2 synthase (mPGES-1) is a potent target for pain and inflammation. Various QSAR (quantitative structure activity relationship) analyses used to understand the factors affecting inhibitory potency for a series of MK886 analogues. We derived four QSAR models utilizing various quantum mechanical (QM) descriptors. These QM models indicate that steric, electrostatic and hydrophobic interaction can be important factors. Common pharmacophore hypotheses (CPHs) also have studied. The QSAR model derived by best-fitted CPHs considering hydrophobic, negative group and ring effect gave a reasonable result (q2 = 0.77, r2 = 0.97 and Rtestset = 0.90). The pharmacophore-derived molecular alignment subsequently used for 3D-QSAR. The CoMFA (Comparative Molecular Field Analysis) and CoMSIA (Comparative Molecular Similarity Indices Analysis) techniques employed on same series of mPGES-1 inhibitors which gives a statistically reasonable result (CoMFA; q2 = 0.90, r2 = 0.99. CoMSIA; q2 = 0.93, r2 = 1.00). All modeling results (QM-based QSAR, pharmacophore modeling and 3D-QSAR) imply steric, electrostatic and hydrophobic contribution to the inhibitory activity. CoMFA and CoMSIA models suggest the introduction of bulky group around ring B may enhance the inhibitory activity.

• The Korean Journal of Pesticide Science
• /
• v.11 no.2
• /
• pp.72-81
• /
• 2007

Quantitative structure-activity relationships (QSARs) on the pre-emergency herbicidal activity and reactivity of a series of new O,O-dialkyl-1-phenoxyacetoxy-1-methylphosphonates (S) analogues against seed of cucumber (Cucumus Sativa) were discussed quantitatively using 2D-QSAR and HQSAR methods. The statistical values of HQSAR model were better than that of 2D-QSAR model. From the frontier molecular orbital (FMO) interaction between substrate molecule (S) and $BH^+$ ion (I) in PDH enzyme, the electrophilic reaction was superior in reactivity. From the effect of substituents, $R_2$-groups in substrate molecule (S) contributed to electrophilic reaction with carbonyl oxygen atom while X, Y-groups contributed to nucleophilic reaction with carbonyl carbon atom. And the influence of X,Y-groups was more effective than that of $R_2$-groups. As a results of 2D-QSAR model (I & II) and atomic contribution maps with HQSAR model, the more length of X, Y-groups is longer, the more herbicidal activity tends to increased. And also, the optimal ${\epsilon}LUMO$ energy, $({\epsilon}LUMO)_{opt.}$=-0.479 (e.v.) of substrate molecule is important factor in determining the herbicidal activity. It is predicted that the herbicidal activity proceeds through a nucleophilic reaction. From the analytical results of 2D-QSAR and HQSAR model, it is suggested that the structural distinctions and descriptors that contribute to herbicidal activities will be able to applied new herbicide design.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.5
• /
• pp.1355-1360
• /
• 2010

In order to search new inhibitors against farnesyl protein transferase (FPTase), a series of 2,3-bis-benzylidenesuccinaldehyde derivatives (1-29) were synthesized and their inhibition activities ($pI_{50}$) against FPTase were measured. From based on the reported results that the inhibitory activities of dimers 2,3-bis-benzylidenesuccinaldehydes were higher than those of monomers cinnamaldehydes, 3D-QSARs on FPTase inhibitory activities of the dimers (1-29) were studied quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The statistical qualities of the optimized CoMFA model II ($r^2{_{cv.}}$= 0.693 and $r^2{_{ncv.}}$= 0.974) was higher than those of the CoMSIA model II ($r^2{_{cv.}}$ = 0.484 and $r^2{_{ncv.}}$ = 0.928). The dependence of CoMFA models on chance correlations was evaluated with progressive scrambling analyses. And the inhibitory activity exhibited a strong correlation with steric factors of the substrate molecules. Therefore, from the results of graphical analyses on the contour maps and of predicted higher inhibitory active compounds, it is suggested that the structural distinctions and descriptors that contribute to inhibitory activities ($pI_{50}$) against FPTase will be able to applied new inhibitor design.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2004.11a
• /
• pp.210-218
• /
• 2004

Poly(ADP-ribose)polymerase-1 (PARP-1) is a nuclear enzyme involved in various physical functions related to genomic repair, and PARP inhibitors have therapeutic application in a variety of neurological diseases. Docking and the QSAR (quantitative structure-activity relationships) studies for 52 PARP-1 inhibitors were conducted using FlexX algorithm, comparative molecular field analysis (CoMFA), and hologram quantitative structure-activity relationship analysis (HQSAR). The resultant FlexX model showed a reasonable correlation (r$^{2}$ = 0.701) between predicted activity and observed activity. Partial least squares analysis produced statistically significant models with q$^{2}$ values of 0.795 (SDEP=0.690, r$^{2}$=0.940, s=0.367) and 0.796 (SDEP=0.678, r$^{2}$ = 0.919, s=0.427) for CoMFA and HQSAR, respectively. The models for the entire inhibitor set were validated by prediction test and scrambling in both QSAR methods. In this work, combination of docking, CoMFA with 3D descriptors and HQSAR based on molecular fragments provided an improved understanding in the interaction between the inhibitors and the PARP. This can be utilized for virtual screening to design novel PARP-1 inhibitors.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.5
• /
• pp.1361-1367
• /
• 2010

A series of O,O-dialkyl-1-phenoxyacetoxy-1-methylphosphonate analogues (1~22) as a new class of potent inhibitors of pyruvate dehydrogenase were synthesized and 3D-QSARs (three dimensional qantitative structure-activity relationships) models on the pre-emergency herbicidal activity against the seed of cucumber (Cucumus Sativa L.) were derived and discussed quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indeces analysis (CoMSIA) methods. The statistical values of CoMSIA models were better predictability and fitness than those of CoMFA models. The inhibitory activities according to the optimized CoMSIA model I were dependent on the electrostatic field (41.4%), the H-bond acceptor field (26.0%), the hydrophobic field (20.8%) and the steric field (11.7%). And also, it was found that the optimized CoMSIA model I with the sensitivity to the perturbation ($d_q{^{2'}}/dr^2{_{yy'}}$ = 0.830) and the prediction ($q^2$ = 0.503) produced by a progressive scrambling analyses were not dependent on chance correlation. From the results of graphical analyses on the contour maps with the optimized CoMSIA model I, it is expected that the structural distinctions and descriptors that subscribe to herbicidal activities will be able to apply new an herbicide design.

• Journal of Digital Contents Society
• /
• v.10 no.3
• /
• pp.423-431
• /
• 2009

There are various image retrieval methods using shape, color and texture features. One of the most active area is using shape and color information. A number of shape representations have been suggested to recognize shapes even under affine transformation. There are many kinds of method for shape recognition, the well-known method is Fourier descriptors and moment invariant. The other method is CSS(Curvature Scale Space). The maxima of curvature scale space image have already been used to represent 2-D shapes in different applications. Because preexistence CSS exists several problems, in this paper we use improved CSS method for retrieval image. There are two kinds of method, One is using RGB color information feature and the other is using HSI color information feature. In this paper we used HSI color model to represent color histogram before, then use it as comparison measure. The similarity is measured by using Euclidean distance and for reduce search time and accuracy, We use DTW for measure similarity. Compare with the result of using Euclidean distance, we can find efficiency elevated.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.855-861
• /
• 2012

A pioneering version of an on-line management system for high-energy molecules (MS-HEMs) was developed by the ADD and BMDRC in Korea. The current system can manage the physicochemical and explosive properties of virtual and existing HEMs. The on-line MS-HEMs consist of three main routines: management, calculation, and search. The management routine contains a user-friendly interface to store and manage molecular structures and other properties of the new HEMs. The calculation routine automatically calculates a number of compositional and topological molecular descriptors when a new HEM is stored in the MS-HEMs. Physical properties, such as the heat of formation and density, can also be calculated using group additivity methods. In addition, the calculation routine for the impact sensitivity can be used to obtain the safety nature of new HEMs. The impact sensitivity was estimated in a knowledge-based manner using in-house neural network code. The search routine enables general users to find an exact HEM and its properties by sketching a 2D chemical structure, or to retrieve HEMs and their properties by giving a range of properties. These on-line MS-HEMs are expected be powerful tool for deriving novel promising HEMs.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• v.11 no.1
• /
• pp.302-320
• /
• 2017

In this paper, an innovative robust feature detection and matching strategy for visual odometry based on stereo image sequence is proposed. First, a sparse multiscale 2D local invariant feature detection and description algorithm AKAZE is adopted to extract the interest points. A robust feature matching strategy is introduced to match AKAZE descriptors. In order to remove the outliers which are mismatched features or on dynamic objects, an improved random sample consensus outlier rejection scheme is presented. Thus the proposed method can be applied to dynamic environment. Then, geometric constraints are incorporated into the motion estimation without time-consuming 3-dimensional scene reconstruction. Last, an iterated sigma point Kalman Filter is adopted to refine the motion results. The presented ego-motion scheme is applied to benchmark datasets and compared with state-of-the-art approaches with data captured on campus in a considerably cluttered environment, where the superiorities are proved.