Displaying publications 1 - 20 of 192 in total

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  1. Dynamic kinetic resolution: alternative approach in optimizing S-ibuprofen production
    Fazlena H, Kamaruddin AH, Zulkali MM
    Bioprocess Biosyst Eng, 2006 Mar;28(4):227-33.
    PMID: 16215728
    A lipase catalysed enantioselective hydrolysis process under in situ racemization of the remaining (R)-ibuprofen ester substrate with sodium hydroxide as the catalyst was developed for the production of S-ibuprofen from (R,S)-ibuprofen ester in isooctane. Detailed investigations on parameters study indicated that 0.5 M NaOH, addition of 20% (v/v) co-solvent (dimethyl sulphoxide), operating temperature of 45 degrees C, and 40 mmol/L substrate gave 86% conversion and 99.4% optical purity of S-ibuprofen in dynamic kinetic resolution. Meanwhile, in common enzymatic kinetic resolution process, only 42% conversion of the racemate and 93% enantiomeric excess of the product was obtained which are of lower values as compared to dynamic kinetic resolution. The S-ibuprofen produced during each process was evaluated and approximately 50% increment in concentration of S-acid product was produced when dynamic kinetic resolution was applied into the process.
    Matched MeSH terms: Models, Chemical*
  2. Near-infrared spectroscopy (NIRS) and chemometric analysis of Malaysian and UK paracetamol tablets: a spectral database study
    Said MM, Gibbons S, Moffat AC, Zloh M
    Int J Pharm, 2011 Aug 30;415(1-2):102-9.
    PMID: 21645600 DOI: 10.1016/j.ijpharm.2011.05.057
    The influx of medicines from different sources into healthcare systems of developing countries presents a challenge to monitor their origin and quality. The absence of a repository of reference samples or spectra prevents the analysis of tablets by direct comparison. A set of paracetamol tablets purchased in Malaysian pharmacies were compared to a similar set of sample purchased in the UK using near-infrared spectroscopy (NIRS). Additional samples of products containing ibuprofen or paracetamol in combination with other actives were added to the study as negative controls. NIR spectra of the samples were acquired and compared by using multivariate modeling and classification algorithms (PCA/SIMCA) and stored in a spectral database. All analysed paracetamol samples contained the purported active ingredient with only 1 out of 20 batches excluded from the 95% confidence interval, while the negative controls were clearly classified as outliers of the set. Although the substandard products were not detected in the purchased sample set, our results indicated variability in the quality of the Malaysian tablets. A database of spectra was created and search methods were evaluated for correct identification of tablets. The approach presented here can be further developed as a method for identifying substandard pharmaceutical products.
    Matched MeSH terms: Models, Chemical
  3. Modeling of reaction kinetics for transesterification of palm-based methyl esters with trimethylolpropane
    Kamil RN, Yusup S
    Bioresour Technol, 2010 Aug;101(15):5877-84.
    PMID: 20304636 DOI: 10.1016/j.biortech.2010.02.084
    A mathematical model describing chemical kinetics of transesterification of palm-based methyl esters with trimethylolpropane has been developed. The model was developed by utilizing nonlinear regression method, which is an efficient and powerful way to determine rate constants for both forward and reverse reactions. A comparison with previous study which excludes the reverse reactions was made. The model was based on the reverse mechanism of transesterification reactions and describes concentration changes of trimethylolpropane, monoesters and diesters production. The developed model was validated against data from the literature. The reaction rate constants were determined using MATLAB version 7.2 and the ratios of rate constants obtained were well in agreement with those reported in the literature. A good correlation between model simulations and experimental data was observed. It was proven that both methods were able to predict the rate constants with plausible accuracy.
    Matched MeSH terms: Models, Chemical*
  4. The evaluation of various kinetic models for base-catalyzed ethanolysis of palm oil
    Shahla S, Ngoh GC, Yusoff R
    Bioresour Technol, 2012 Jan;104:1-5.
    PMID: 22154586 DOI: 10.1016/j.biortech.2011.11.010
    In this paper, the kinetics of palm oil ethanolysis with various models have been investigated in a temperature range of 25-55 °C. The highest yield was achieved when the conversion to ethyl ester was 97.5±0.5% in the stated temperature range, using ethanol:oil molar ratio of 12:1, and 1.0 wt.% sodium ethoxide. The level of conformity of the reaction with reversible second order, irreversible second order and first order kinetic models were evaluated by means of the R(2) values of the linear curves. The ethanolysis showed the best conformity with irreversible second order kinetic model with 92-98% level of confidence. The reaction rate constants were within 0.018-0.088 dm(3)/mol min and the activation energy of the reaction was 42.36 kJ/mol.
    Matched MeSH terms: Models, Chemical*
  5. Trends in the use of Fenton, electro-Fenton and photo-Fenton for the treatment of landfill leachate
    Umar M, Aziz HA, Yusoff MS
    Waste Manag, 2010 Nov;30(11):2113-21.
    PMID: 20675113 DOI: 10.1016/j.wasman.2010.07.003
    Advanced oxidation processes (AOPs) such as Fenton, electro-Fenton and photo-Fenton have been applied effectively to remove refractory organics from landfill leachate. The Fenton reaction is based on the addition of hydrogen peroxide to the wastewater or leachate in the presence of ferrous salt as a catalyst. The use of this technique has proved to be one of the best compromises for landfill leachate treatment because of its environmental and economical advantages. Fenton process has been used successfully to mineralize wide range of organic constituents present in landfill leachate particularly those recalcitrant to biological degradation. The present study reviews the use of Fenton and related processes in terms of their increased application to landfill leachate. The effects of various operating parameters and their optimum ranges for maximum COD and color removal are reviewed with the conclusion that the Fenton and related processes are effective and competitive with other technologies for degradation of both raw and pre-treated landfill leachate.
    Matched MeSH terms: Models, Chemical
  6. Modeling the relationship between the main emulsion components and stability, viscosity, fluid behavior, zeta-potential, and electrophoretic mobility of orange beverage emulsion using response surface methodology
    Mirhosseini H, Tan CP, Hamid NS, Yusof S
    J Agric Food Chem, 2007 Sep 19;55(19):7659-66.
    PMID: 17708646
    The possible relationships between the main emulsion components (namely, Arabic gum, xanthan gum, and orange oil) and the physicochemical properties of orange beverage emulsion were evaluated by using response surface methodology. The physicochemical emulsion property variables considered as response variables were emulsion stability, viscosity, fluid behavior, zeta-potential, and electrophoretic mobility. The independent variables had the most and least significant ( p < 0.05) effect on viscosity and zeta-potential, respectively. The quadratic effect of orange oil and Arabic gum, the interaction effect of Arabic gum and xanthan gum, and the main effect of Arabic gum were the most significant ( p < 0.05) effects on turbidity loss rate, viscosity, viscosity ratio, and mobility, respectively. The main effect of Arabic gum was found to be significant ( p < 0.05) in all response variables except for turbidity loss rate. The nonlinear regression equations were significantly ( p < 0.05) fitted for all response variables with high R (2) values (>0.86), which had no indication of lack of fit. The results indicated that a combined level of 10.78% (w/w) Arabic gum, 0.56% (w/w) xanthan gum, and 15.27% (w/w) orange oil was predicted to provide the overall optimum region in terms of physicochemical properties studied. No significant ( p > 0.05) difference between the experimental and the predicted values confirmed the adequacy of response surface equations.
    Matched MeSH terms: Models, Chemical
  7. Fulltext The modelled raindrop size distribution of Skudai, Peninsular Malaysia, using exponential and lognormal distributions
    Yakubu ML, Yusop Z, Yusof F
    ScientificWorldJournal, 2014;2014:361703.
    PMID: 25126597 DOI: 10.1155/2014/361703
    This paper presents the modelled raindrop size parameters in Skudai region of the Johor Bahru, western Malaysia. Presently, there is no model to forecast the characteristics of DSD in Malaysia, and this has an underpinning implication on wet weather pollution predictions. The climate of Skudai exhibits local variability in regional scale. This study established five different parametric expressions describing the rain rate of Skudai; these models are idiosyncratic to the climate of the region. Sophisticated equipment that converts sound to a relevant raindrop diameter is often too expensive and its cost sometimes overrides its attractiveness. In this study, a physical low-cost method was used to record the DSD of the study area. The Kaplan-Meier method was used to test the aptness of the data to exponential and lognormal distributions, which were subsequently used to formulate the parameterisation of the distributions. This research abrogates the concept of exclusive occurrence of convective storm in tropical regions and presented a new insight into their concurrence appearance.
    Matched MeSH terms: Models, Chemical*
  8. Fulltext Gold nanoparticle trapping and delivery for therapeutic applications
    Aziz MS, Suwanpayak N, Jalil MA, Jomtarak R, Saktioto T, Ali J, et al.
    Int J Nanomedicine, 2012;7:11-7.
    PMID: 22275818 DOI: 10.2147/IJN.S27417
    A new optical trapping design to transport gold nanoparticles using a PANDA ring resonator system is proposed. Intense optical fields in the form of dark solitons controlled by Gaussian pulses are used to trap and transport nanoscopic volumes of matter to the desired destination via an optical waveguide. Theoretically, the gradient and scattering forces are responsible for this trapping phenomenon, where in practice such systems can be fabricated and a thin-film device formed on the specific artificial medical materials, for instance, an artificial bone. The dynamic behavior of the tweezers can be tuned by controlling the optical pulse input power and parameters of the ring resonator system. Different trap sizes can be generated to trap different gold nanoparticles sizes, which is useful for gold nanoparticle therapy. In this paper, we have shown the utility of gold nanoparticle trapping and delivery for therapy, which may be useful for cosmetic therapy and related applications.
    Matched MeSH terms: Models, Chemical
  9. Carboxymethyl fenugreek galactomannan-g-poly(N-isopropylacrylamide-co-N,N'-methylene-bis-acrylamide)-clay based pH/temperature-responsive nanocomposites as drug-carriers
    Bera H, Abbasi YF, Gajbhiye V, Liew KF, Kumar P, Tambe P, et al.
    Mater Sci Eng C Mater Biol Appl, 2020 May;110:110628.
    PMID: 32204068 DOI: 10.1016/j.msec.2020.110628
    The current study dealt with the synthesis and characterization of carboxymethyl fenugreek galactomannang-g-poly(N-isopropylacrylamide-co-N,N'-methylene-bis-acrylamide)-bentonite [CFG-g-P(NIPA-co-MBA)-BEN] based nanocomposites (NCs) as erlotinib (ERL)-delivery devices for lung cancer cells to suppress excessive cell proliferation. The blank NCs exhibited outstanding biodegradability and pH/temperature-dependent swelling profiles, which were significantly influenced by their BEN contents (0-20%). The molar mass (M¯c) between the crosslinks of these NCs was declined with temperature. The composite architecture of these scaffolds was confirmed by XRD, FTIR, TGA, DSC and SEM analyses. The corresponding ERL-loaded matrices (F-1-F-3) portrayed outstanding drug encapsulation efficiency (DEE, 93-100%) with zeta potential between -8 and -16 mV and diameter between 615 and 1258 nm. These formulations demonstrated sustained ERL elution profiles (Q8h, 62-98%) with an initial burst release of drug. The drug dissolution pattern of the optimized matrices (F-3) obeyed first-order kinetic model and was driven by Fickian diffusion. The mucin adsorption behavior of F-3 was best fitted to Freudlich isotherms. The ERL-loaded formulation suppressed A549 cell proliferation and promoted apoptosis to a greater extent than the pristine drug, as detected by cellular uptake analysis, MTT cytotoxicity test and AO/EB staining assay.
    Matched MeSH terms: Models, Chemical*
  10. Effect of different oxytetracycline addition methods on its degradation behavior in soil
    Chen GX, He WW, Wang Y, Zou YD, Liang JB, Liao XD, et al.
    Sci Total Environ, 2014 May 1;479-480:241-6.
    PMID: 24561929 DOI: 10.1016/j.scitotenv.2014.01.124
    The degradation behavior of veterinary antibiotics in soil is commonly studied using the following methods of adding antibiotics to the soil: (i) adding manure collected from animals fed with a diet containing antibiotics, (ii) adding antibiotic-free animal manure spiked with antibiotics and (iii) directly adding antibiotics. No research simultaneously comparing different antibiotic addition methods was found. Oxytetracycline (OTC) was used as a model antibiotic to compare the effect of the three commonly used antibiotic addition methods on OTC degradation behavior in soil. The three treatment methods have similar trends, though OTC degradation half-lives show the following significant differences (P<0.05): manure from swine fed OTC (treatment A)
    Matched MeSH terms: Models, Chemical
  11. Compost feedstock characteristics and ratio modelling for organic waste materials co-composting in Malaysia
    Chai EW, H'ng PS, Peng SH, Wan-Azha WM, Chin KL, Chow MJ, et al.
    Environ Technol, 2013 Sep-Oct;34(17-20):2859-66.
    PMID: 24527651
    In Malaysia, large amounts of organic materials, which lead to disposal problems, are generated from agricultural residues especially from palm oil industries. Increasing landfill costs and regulations, which limit many types of waste accepted at landfills, have increased the interest in composting as a component of waste management. The objectives of this study were to characterize compost feedstock properties of common organic waste materials available in Malaysia. Thus, a ratio modelling of matching ingredients for empty fruit bunches (EFBs) co-composting using different organic materials in Malaysia was done. Organic waste materials with a C/N ratio of < 30 can be applied as a nitrogen source in EFB co-composting. The outcome of this study suggested that the percentage of EFB ranged between 50% and 60%, which is considered as the ideal mixing ratio in EFB co-composting. Conclusively, EFB can be utilized in composting if appropriate feedstock in term of physical and chemical characteristics is coordinated in the co-composting process.
    Matched MeSH terms: Models, Chemical
  12. Tapered US carbon emissions during good times: what's old, what's new?
    Eng YK, Wong CY
    Environ Sci Pollut Res Int, 2017 Nov;24(32):25047-25060.
    PMID: 28920161 DOI: 10.1007/s11356-017-0144-6
    In light of a slow buildup in CO2 emissions since the recovery, this paper revisits the relationship between CO2 emissions and the US economy using a nonlinear autoregressive distributed lag model, in which the determinants are identified through an expanded real business cycle model. We find convincing evidence that CO2 emissions decline more rapidly during recessions than increase during expansions over the long run. Of all determinants considered, long-run asymmetry is fostered once vehicle miles traveled is controlled. This calls for a greater attention to public transportation development and vehicle miles traveled tax for slowing down stock buildup of CO2 emissions during good times.
    Matched MeSH terms: Models, Chemical
  13. Adsorption of butyl acetate in air over silver-loaded Y and ZSM-5 zeolites: experimental and modelling studies
    Bhatia S, Abdullah AZ, Wong CT
    J Hazard Mater, 2009 Apr 15;163(1):73-81.
    PMID: 18649998 DOI: 10.1016/j.jhazmat.2008.06.055
    Adsorption behaviours of butyl acetate in air have been studied over silver-loaded Y (Si/Al=40) and ZSM-5 (Si/Al=140) zeolites. The silver metal was loaded into the zeolites by ion exchange (IE) and impregnation (IM) methods. The adsorption study was mainly conducted at a gas hourly space velocity (GHSV) of 13,000 h(-1) with the organic concentration of 1000 ppm while the desorption step was carried out at a GHSV of 5000 h(-1). The impregnated silver-loaded adsorbents showed lower uptake capacity and shorter breakthrough time by about 10 min, attributed to changes in the pore characteristics and available surface for adsorption. Silver exchanged Y (AgY(IE)) with lower hydrophobicity showed higher uptake capacity of up to 35%, longer adsorbent service time and easier desorption compared to AgZSM-5(IE). The presence of water vapour in the feed suppressed the butyl acetate adsorption of AgY(IE) by 42% due to the competitive adsorption of water on the surface and the effect was more pronounced at lower GHSV. Conversely, the adsorption capacity of AgZSM-5(IE) was minimally affected, attributed to the higher hydrophobicity of the material. A mathematical model is proposed to simulate the adsorption behaviour of butyl acetate over AgY(IE) and AgZSM-5(IE). The model parameters were successfully evaluated and used to accurately predict the breakthrough curves under various process conditions with root square mean errors of between 0.05 and 0.07.
    Matched MeSH terms: Models, Chemical*
  14. Fulltext Kinetics and Optimization of Lipophilic Kojic Acid Derivative Synthesis in Polar Aprotic Solvent Using Lipozyme RMIM and Its Rheological Study
    Ishak N, Lajis AFB, Mohamad R, Ariff AB, Mohamed MS, Halim M, et al.
    Molecules, 2018 Feb 24;23(2).
    PMID: 29495254 DOI: 10.3390/molecules23020501
    The synthesis of kojic acid derivative (KAD) from kojic and palmitic acid (C16:0) in the presence of immobilized lipase from Rhizomucor miehei (commercially known as Lipozyme RMIM), was studied using a shake flask system. Kojic acid is a polyfunctional heterocycles that acts as a source of nucleophile in this reaction allowing the formation of a lipophilic KAD. In this study, the source of biocatalyst, Lipozyme RMIM, was derived from the lipase of Rhizomucor miehei immobilized on weak anion exchange macro-porous Duolite ES 562 by the adsorption technique. The effects of solvents, enzyme loading, reaction temperature, and substrate molar ratio on the reaction rate were investigated. In one-factor-at-a-time (OFAT) experiments, a high reaction rate (30.6 × 10-3 M·min-1) of KAD synthesis was recorded using acetone, enzyme loading of 1.25% (w/v), reaction time of 12 h, temperature of 50 °C and substrate molar ratio of 5:1. Thereafter, a yield of KAD synthesis was optimized via the response surface methodology (RSM) whereby the optimized molar ratio (fatty acid: kojic acid), enzyme loading, reaction temperature and reaction time were 6.74, 1.97% (w/v), 45.9 °C, and 20 h respectively, giving a high yield of KAD (64.47%). This condition was reevaluated in a 0.5 L stirred tank reactor (STR) where the agitation effects of two impellers; Rushton turbine (RT) and pitch-blade turbine (PBT), were investigated. In the STR, a very high yield of KAD synthesis (84.12%) was achieved using RT at 250 rpm, which was higher than the shake flask, thus indicating better mixing quality in STR. In a rheological study, a pseudoplastic behavior of KAD mixture was proposed for potential application in lotion formulation.
    Matched MeSH terms: Models, Chemical
  15. Surface phonon polariton characteristics of In(0.04)Al(0.06)Ga(0.90)N/AlN/Al(2)O(3) heterostructure
    Ng SS, Lee SC, Bakhori SK, Hassan Z, Abu Hassan H, Yakovlev VA, et al.
    Opt Express, 2010 May 10;18(10):10354-9.
    PMID: 20588890 DOI: 10.1364/OE.18.010354
    Surface phonon polariton (SPP) characteristics of In(0.04)Al(0.06)Ga(0.90)N/AlN/Al(2)O(3) heterostructure are investigated by means of p-polarized infrared (IR) attenuated total reflection spectroscopy. Two absorption dips corresponding to In(0.04)Al(0.06)Ga(0.90)N SPP modes are observed. In addition, two prominent dips and one relatively weak and broad dip corresponding to the Al(2)O(3) SPP mode, In(0.04)Al(0.06)Ga(0.90)N/Al(2)O(3) interface mode, and Al(2)O(3) bulk polariton mode, respectively, are clearly seen. No surface mode feature originating from the AlN layer is observed because it is too thin. Overall, the observations are in good agreement with the theoretical predictions.
    Matched MeSH terms: Models, Chemical
  16. Enzymatic synthesis of farnesyl laurate in organic solvent: initial water activity, kinetics mechanism, optimization of continuous operation using packed bed reactor and mass transfer studies
    Rahman NK, Kamaruddin AH, Uzir MH
    Bioprocess Biosyst Eng, 2011 Aug;34(6):687-99.
    PMID: 21327986 DOI: 10.1007/s00449-011-0518-y
    The influence of water activity and water content was investigated with farnesyl laurate synthesis catalyzed by Lipozyme RM IM. Lipozyme RM IM activity depended strongly on initial water activity value. The best results were achieved for a reaction medium with an initial water activity of 0.11 since it gives the best conversion value of 96.80%. The rate constants obtained in the kinetics study using Ping-Pong-Bi-Bi and Ordered-Bi-Bi mechanisms with dead-end complex inhibition of lauric acid were compared. The corresponding parameters were found to obey the Ordered-Bi-Bi mechanism with dead-end complex inhibition of lauric acid. Kinetic parameters were calculated based on this model as follows: V (max) = 5.80 mmol l(-1) min(-1) g enzyme(-1), K (m,A) = 0.70 mmol l(-1) g enzyme(-1), K (m,B) = 115.48 mmol l(-1) g enzyme(-1), K (i) = 11.25 mmol l(-1) g enzyme(-1). The optimum conditions for the esterification of farnesol with lauric acid in a continuous packed bed reactor were found as the following: 18.18 cm packed bed height and 0.9 ml/min substrate flow rate. The optimum molar conversion of lauric acid to farnesyl laurate was 98.07 ± 0.82%. The effect of mass transfer in the packed bed reactor has also been studied using two models for cases of reaction limited and mass transfer limited. A very good agreement between the mass transfer limited model and the experimental data obtained indicating that the esterification in a packed bed reactor was mass transfer limited.
    Matched MeSH terms: Models, Chemical
  17. Molecular Structures of Isomeric Ortho, Meta, and Para Bromo-Substituted α-Methylsulfonyl-α-diethoxyphosphoryl Acetophenones by X-ray and DFT Molecular Orbital Calculations
    Rodrigues A, Olivato PR, Zukerman-Schpector J, Maganhi SH, Reis AK, Tiekink ER
    J Phys Chem A, 2015 Aug 13;119(32):8714-23.
    PMID: 26213179 DOI: 10.1021/acs.jpca.5b04019
    The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.
    Matched MeSH terms: Models, Chemical
  18. Fulltext Cyclization vs. cyclization/dimerization in o-amidostilbene radical cation cascade reactions: the amide question
    Kee CH, Ariffin A, Awang K, Noorbatcha I, Takeya K, Morita H, et al.
    Molecules, 2011 Aug 25;16(9):7267-87.
    PMID: 21869754 DOI: 10.3390/molecules16097267
    The n-butyramido, isobutyramido, benzamido, and furancarboxamido functions profoundly modulate the electronics of the stilbene olefinic and NH groups and the corresponding radical cations in ways that influence the efficiency of the cyclization due presumably to conformational and stereoelectronic factors. For example, isobutyramido- stilbene undergoes FeCl(3) promoted cyclization to produce only indoline, while n-butyramidostilbene, under the same conditions, produces both indoline and bisindoline.
    Matched MeSH terms: Models, Chemical
  19. Analysis of model-based and model-free CEST effect quantification methods for different medical applications
    Foo LS, Yap WS, Hum YC, Manan HA, Tee YK
    J Magn Reson, 2020 01;310:106648.
    PMID: 31760147 DOI: 10.1016/j.jmr.2019.106648
    Chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) holds great potential to provide new metabolic information for clinical applications such as tumor, stroke and Parkinson's Disease diagnosis. Many active research and developments have been conducted to translate this emerging MRI technique for routine clinical applications. In general, there are two CEST quantification techniques: (i) model-free and (ii) model-based techniques. The reliability of these quantification techniques depends heavily on the experimental conditions and quality of the collected data. Errors such as noise may lead to misleading quantification results and thus inaccurate diagnosis when CEST imaging becomes a standard or routine imaging scan in the future. This paper investigates the accuracy and robustness of these quantification techniques under different signal-to-noise (SNR) levels and magnetic field strengths. The quantified CEST effect before and after adding random Gaussian White Noise using model-free and model-based quantification techniques were compared. It was found that the model-free technique consistently yielded larger average percentage error across all tested parameters compared to its model-based counterpart, and that the model-based technique could withstand SNR of about 3 times lower than the model-free technique. When applied on noisy brain tumor, ischemic stroke, and Parkinson's Disease clinical data, the model-free technique failed to produce significant differences between normal and abnormal tissue whereas the model-based technique consistently generated significant differences. Although the model-free technique was less accurate and robust, its simplicity and thus speed would still make it a good approximate when the SNR was high (>50) or when the CEST effect was large and well-defined. For more accurate CEST quantification, model-based techniques should be considered. When SNR was low (<50) and the CEST effect was small such as those acquired from clinical field strength scanners, which are generally 3T and below, model-based techniques should be considered over model-free counterpart to maintain an average percentage error of less than 44% even under very noisy condition as tested in this work.
    Matched MeSH terms: Models, Chemical
  20. Fulltext AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
    Wisitponchai T, Shoombuatong W, Lee VS, Kitidee K, Tayapiwatana C
    BMC Bioinformatics, 2017 Apr 19;18(1):220.
    PMID: 28424069 DOI: 10.1186/s12859-017-1628-6
    BACKGROUND: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet.

    RESULTS: In this study, we established an ensemble computational model for discriminating the near-native docking pose of APKs named "AnkPlex". A dataset of APKs was generated from seven X-ray APKs, which consisted of 3 internal domains, using the reliable docking tool ZDOCK. The dataset was composed of 669 and 44,334 near-native and non-near-native poses, respectively, and it was used to generate eleven informative features. Subsequently, a re-scoring rank was generated by AnkPlex using a combination of a decision tree algorithm and logistic regression. AnkPlex achieved superior efficiency with ≥1 near-native complexes in the 10 top-rankings for nine X-ray complexes compared to ZDOCK, which only obtained six X-ray complexes. In addition, feature analysis demonstrated that the van der Waals feature was the dominant near-native pose out of the potential ankyrin-protein docking poses.

    CONCLUSION: The AnkPlex model achieved a success at predicting near-native docking poses and led to the discovery of informative characteristics that could further improve our understanding of the ankyrin-protein complex. Our computational study could be useful for predicting the near-native poses of binding proteins and desired targets, especially for ankyrin-protein complexes. The AnkPlex web server is freely accessible at http://ankplex.ams.cmu.ac.th .

    Matched MeSH terms: Models, Chemical*
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