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1.

Background  

Secondary structure prediction is a useful first step toward 3D structure prediction. A number of successful secondary structure prediction methods use neural networks, but unfortunately, neural networks are not intuitively interpretable. On the contrary, hidden Markov models are graphical interpretable models. Moreover, they have been successfully used in many bioinformatic applications. Because they offer a strong statistical background and allow model interpretation, we propose a method based on hidden Markov models.  相似文献   

2.
Carcinogenicity is one of the toxicological endpoints causing the highest concern. Also, the standard bioassays in rodents used to assess the carcinogenic potential of chemicals and drugs are extremely long, costly and require the sacrifice of large numbers of animals. For these reasons, we have attempted development of a global quantitative structure-activity relationship (QSAR) model using a data set of 1464 compounds (the Galvez data set available from http://www.uv.es/-galvez/tablevi.pdf), including many marketed drugs for their carcinogenesis potential. Though experimental toxicity testing using animal models is unavoidable for new drug candidates at an advanced stage of drug development, yet the developed global QSAR model can in silico predict the carcinogenicity of new drug compounds to provide a tool for initial screening of new drug candidate molecules with reduced number of animal testing, money and time. Considering large number of data points with diverse structural features used for model development (n(training) = 732) and model validation (n(test) = 732), the model developed in this study has an encouraging statistical quality (leave-one-out Q2 = 0.731, R2pred = 0.716). Our developed model suggests that higher lipophilicity values and conjugated ring systems, thioketo and nitro groups contribute positively towards drug carcinogenicity. On the contrary, tertiary and secondary nitrogens, phenolic, enolic and carboxylic OH fragments and presence of three-membered rings reduce the carcinogenicity. Branching, size and shape are found to be crucial factors for drug-induced carcinogenicity. One may consider all these points to reduce carcinogenic potential of the molecules.  相似文献   

3.
A model is introduced for the motor program which controls final position. The first part of the model relates the biomechanical properties of the muscles to the EMG activities of the extensor and flexor muscles and thereby generates quatitative predictions for the relationships between the EMGs, final position, external forces, muscle stiffness, and muscle tension. To the extent that comparable data exist, the model is shown to give correct quantitative predictions. When only qualitative comparisons can be made, the model is consistent with the data in the literature. The model is complete and can be tested quantitatively in detail in the future. An equivalent circuit for the neural network that innervates the muscles is given. It is shown to have the advantages of making the programming of final position simple to either compute or lookup in a table. In addition, new situations, such as adapting to a force, or an unusual viewing angle, lead to very simple changes in the basic program in terms of the equivalent circuit.  相似文献   

4.
The prediction of transmembrane protein sequences can be performed with reasonable accuracy. However, the prediction of their conformation leaves room for significant improvement.  相似文献   

5.
A finite element (FE) model of a 10-years-old child pelvis was developed and validated against experimental data from lateral impacts of pediatric pelves. The pelvic bone geometry was reconstructed from a set of computed tomography images, and a hexahedral mesh was generated using a new octree-based hexahedral meshing technique. Lateral impacts to the greater trochanter and iliac wing of the seated pelvis were simulated. Sensitivity analysis was conducted to identify material parameters that substantially affected the model response. An optimization-based material identification method was developed to obtain the most favorable material property set by minimizing differences in biomechanical responses between experimental and simulation results. This study represents a pilot effort in the development and validation of age-dependent musculoskeletal FE models for children, which may ultimately serve to evaluate injury mechanisms and means of protection for the pediatric population.  相似文献   

6.
SUMMARY: Recent advances in high-throughput technology have increased the quantity of available data on protein complexes and stimulated the development of many new prediction methods. In this article, we present ProCope, a Java software suite for the prediction and evaluation of protein complexes from affinity purification experiments which integrates the major methods for calculating interaction scores and predicting protein complexes published over the last years. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework. AVAILABILITY: Source code and executables are available at http://www.bio.ifi.lmu.de/Complexes/ProCope/.  相似文献   

7.
Protein complexes play a dominant role in cellular organization and function. Prediction of protein complexes from the network of physical interactions between proteins (PPI networks) has thus become one of the important research areas. Recently, many computational approaches have been developed to identify these complexes. Various performance assessment measures have been proposed for evaluating the efficiency of these methods. However, there are many inconsistencies in the definitions and usage of the measures across the literature. To address this issue, we have gathered and presented the most important performance evaluation measures and developed a tool, named CompEvaluator, to critically assess the protein complex prediction methods. The tool and documentation are publicly available at https://sourceforge.net/projects/compevaluator/files/.  相似文献   

8.
【目的】随着转基因棉种植年限的延长,绿盲蝽Apolygus lucorum(Meyer-Dür)成为棉田主要害虫,建立准确的预测预报模型,可为绿盲蝽的防控奠定基础。【方法】通过收集整理基点16年(1993—2008年)绿盲蝽各代成若虫的发生高峰期与发生量以及平均气温、相对湿度、降雨量、雨日、光照时数等各项因子数据,利用DPSv8.05专业版数据处理系统,采用多因子逐步回归方法,从各代发生量、平均温度、雨量、湿度、光照时长等因子中筛选出4~5个相关显著的预测因子进一步用二次多项回归建立预测模型。【结果】初步建立了绿盲蝽各代发生期、发生量预测模型,进行了回代检验,并进一步利用6年(2009—2014年)的绿盲蝽实际发生数据对预测模型的应用效果就行了外延检测,总体测报准确率平均达到85%以上。【结论】建立的绿盲蝽中期测报模型准确率较高,农业技术推广部门可以在绿盲蝽的预测预报工作中加以应用。  相似文献   

9.
We describe the development and use of the first mathematical computer model for a polar lake. This dynamic model graphically illustrates seasonal and annual predictions of the changes in the biomass of plankton and attached primary producers, decomposers and consumers, changes in the quantities of potential nutrients and organic matter. The model consists of 100 submodels of which 79 are algebraic equations and 21 are differential equations. It has proven valuable as a means of identifying voids in our limnological program and probable errors in field measurements.Department of StatisticsDepartment of Biology  相似文献   

10.
Linsong Dong  Zhiyong Wang 《Genetica》2018,146(4-5):361-368
Genomic prediction is feasible for estimating genomic breeding values because of dense genome-wide markers and credible statistical methods, such as Genomic Best Linear Unbiased Prediction (GBLUP) and various Bayesian methods. Compared with GBLUP, Bayesian methods propose more flexible assumptions for the distributions of SNP effects. However, most Bayesian methods are performed based on Markov chain Monte Carlo (MCMC) algorithms, leading to computational efficiency challenges. Hence, some fast Bayesian approaches, such as fast BayesB (fBayesB), were proposed to speed up the calculation. This study proposed another fast Bayesian method termed fast BayesC (fBayesC). The prior distribution of fBayesC assumes that a SNP with probability γ has a non-zero effect which comes from a normal density with a common variance. The simulated data from QTLMAS XII workshop and actual data on large yellow croaker were used to compare the predictive results of fBayesB, fBayesC and (MCMC-based) BayesC. The results showed that when γ was set as a small value, such as 0.01 in the simulated data or 0.001 in the actual data, fBayesB and fBayesC yielded lower prediction accuracies (abilities) than BayesC. In the actual data, fBayesC could yield very similar predictive abilities as BayesC when γ?≥?0.01. When γ?=?0.01, fBayesB could also yield similar results as fBayesC and BayesC. However, fBayesB could not yield an explicit result when γ?≥?0.1, but a similar situation was not observed for fBayesC. Moreover, the computational speed of fBayesC was significantly faster than that of BayesC, making fBayesC a promising method for genomic prediction.  相似文献   

11.
 In this paper maximal performance posture control of the human arm is investigated by means of model simulations. Recent experiments (F.C.T. van der Helm, submitted, 2000) have shown that the reflexive feedback during postural control varies with the bandwidth of the applied force disturbances. This paper focusses on the influence of the frequency content of force disturbances on the reflexive feedback gains by means of optimization. The arm is modelled by a non-linear musculo-skeletal model with two degrees of freedom and six muscles. To facilitate the optimization of the model parameters, the arm model is linearized. A performance criterion is minimized for stochastic force disturbances in a two-step procedure: (1) optimization of static muscle activations using an additional energy criterion to obtain a unique and energy-efficient solution; and (2) optimization of reflex gains using an additional control effort criterion to obtain a unique solution. The optimization reveals that for the given task and posture, the shoulder muscles have the largest contribution, whereas the bi-articular muscles have a relatively small contribution to the behaviour. The dynamics at the endpoint level are estimated so that a comparison can be made with the experiments. Compared to the experiments, the intrinsic damping of the model is relatively large (about 150%), whereas the intrinsic stiffness is relatively small (about 60%). These differences can be attributed to unmodelled mechanical effects of cross-bridges in Hill-type muscle models. The optimized reflex gains show remarkable similarities with the values found in the experiments, implying that humans can adjust their reflexive feedback gains in an optimal way, weighting the performance and energy. The approach in this paper could be useful in the study of various posture tasks, for example in the prediction of the relation between the control parameters of various musculo-skeletal models and different experimental variables. Received: 24 January 2000 / Accepted in revised form: 7 July 2000  相似文献   

12.
13.
On-farm cultivation of phototrophic, N-fixing cyanobacteria, grown in raceway ponds, could provide organic farmers an alternative N source to meet crop fertilizer needs. The application of cyanobacterial fertilizer in certified organic agriculture requires a growth medium of certified organic ingredients. This study compared growth and N-fixation of cyanobacteria cultured in two media, Allen and Arnon (AA) and a growth medium of organic-approved ingredients (RB) developed by the authors. A xenic culture of Anabaena sp. was grown for 2 weeks in the laboratory. The RB medium had significantly lower concentrations of P, Fe, B, Zn, and Cu than the AA medium. Cyanobacteria grown in RB had significantly greater exponential growth rate but significantly lower net total Kjeldahl nitrogen (TKN) than those grown in AA. In a follow-up replicated field study, the xenic culture of Anabaena sp. was inoculated into raceways aerated by paddle wheels. There was no significant difference in exponential or linear growth rate between the two treatments though the RB medium had lower concentrations of P, Co, Zn, and B than the AA medium. The lack of difference could be the result of an overarching limiting factor evident in both treatments such as light or C depletion or that the lower nutrient concentrations in RB were still sufficient for growth and N-fixation. There was no difference in net TKN between the two treatments, suggesting similar rates of N-fixation. Since bone meal contributed trace amounts of N to the RB media, it is possible that maximal N-fixation was not achieved. However, RB medium was able to support growth similar to that of the AA medium in raceway cultivation.  相似文献   

14.
The purpose of this study was to develop a model for assessing the ecological value of a dam reservoir. Various evaluable characteristics (“elements”) that influence the ecology of the target area around the dam were grouped into three classes: (1) physical elements, such as altitude, slope, and aspect; (2) vegetation elements, such as forest physiognomy, vegetation type, age class, diameter at breast height (DBH) class, and density; and (3) habitat elements, such as ecological conditions, vegetation conservation classification, and frequency of wildlife appearances. The evaluation standard was quantified considering the ecological function of each element. The developed assessment model was applied to the Yeongju Dam in the Nakdong River basin in Korea. This study assumed that the ecological condition before the dam construction was 100 %. The results of this study showed that the physical, vegetation, and habitat elements were downgraded to 82.8, 95.5, and 90.7 %, respectively, after the construction of the dam. The overall ecological value was estimated to be 90.0 % and thus decreased by 10.0 % due to dam construction. Additionally, by combining the results for the evaluation elements, an ecologically healthy area was selected. The results of this study should prove useful for quantifying ecological impact and for establishing an ecological restoration plan for dam reservoirs.  相似文献   

15.
16.
A multivariate prediction model for microarray cross-hybridization   总被引:1,自引:0,他引:1  

Background  

Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of potential cross-hybridization. This is a pervasive problem for both oligonucleotide and cDNA microarrays; it is considered particularly problematic for the latter. No comprehensive multivariate predictive modeling has been performed to understand how multiple variables contribute to (cross-) hybridization.  相似文献   

17.

Background  

The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. Although considerable progress has been made recently in understanding how the RNAi pathway mediates gene silencing, the design of potent siRNAs remains challenging.  相似文献   

18.
19.
An accelerated storage test was carried out on freeze-dried samples of five variants of tomato mosaic virus – from leaf material, plant sap and purified preparation with and without protectant, at 28, 37 and 45 °C. A model for longevity prediction of lyophilized tobamoviruses was developed. The preservation of tomato mosaic virus decreased to 10% after 0.7–2.8 years in unprotected variants and after 7.5–11 years in protected samples under real storage conditions. Experimental data have confirmed the predicted values.  相似文献   

20.
Traditional statistical models for the prediction of peptide helicity are written in terms of the mean fractional helicity of the peptide residues. Far ultraviolet circular dichroic measurements of peptide solutions are converted to mean fractional helicity by partitioning the observed ellipticity between that of a perfect helix and a random coil. This partition does not adequately represent the ensemble of peptide molecules present in solution that populate imperfect helical conformations of quite variable lengths. A new dichroic statistical model has been written in terms of ellipticity rather than fractional helical content that recognizes (1) the source of ellipticity, peptide bond adsorption; (2) the differential ellipticity of peptide bonds in the terminal and interior helical turns; and (3) the contributions of each participant in a conformational ensemble to the observed ellipticity. Comparative analyses of host/guest peptides indicates that significant differences are obtained between residue w and n weights and ellipticity values using the traditional and dichroic statistical models. Proteins 28:467–480, 1997. © 1997 Wiley-Liss, Inc.  相似文献   

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