Search results for: Protein data bank
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 7845

Search results for: Protein data bank

7845 An Algebra for Protein Structure Data

Authors: Yanchao Wang, Rajshekhar Sunderraman

Abstract:

This paper presents an algebraic approach to optimize queries in domain-specific database management system for protein structure data. The approach involves the introduction of several protein structure specific algebraic operators to query the complex data stored in an object-oriented database system. The Protein Algebra provides an extensible set of high-level Genomic Data Types and Protein Data Types along with a comprehensive collection of appropriate genomic and protein functions. The paper also presents a query translator that converts high-level query specifications in algebra into low-level query specifications in Protein-QL, a query language designed to query protein structure data. The query transformation process uses a Protein Ontology that serves the purpose of a dictionary.

Keywords: Domain-Specific Data Management, Protein Algebra, Protein Ontology, Protein Structure Data.

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7844 Using Spectral Vectors and M-Tree for Graph Clustering and Searching in Graph Databases of Protein Structures

Authors: Do Phuc, Nguyen Thi Kim Phung

Abstract:

In this paper, we represent protein structure by using graph. A protein structure database will become a graph database. Each graph is represented by a spectral vector. We use Jacobi rotation algorithm to calculate the eigenvalues of the normalized Laplacian representation of adjacency matrix of graph. To measure the similarity between two graphs, we calculate the Euclidean distance between two graph spectral vectors. To cluster the graphs, we use M-tree with the Euclidean distance to cluster spectral vectors. Besides, M-tree can be used for graph searching in graph database. Our proposal method was tested with graph database of 100 graphs representing 100 protein structures downloaded from Protein Data Bank (PDB) and we compare the result with the SCOP hierarchical structure.

Keywords: Eigenvalues, m-tree, graph database, protein structure, spectra graph theory.

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7843 Protein-Protein Interaction Detection Based on Substring Sensitivity Measure

Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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7842 Impacts of Financial Development and Operating Scale on Bank Efficiencies in Taiwan

Authors: Ying-Hsiu Chen, Pao-Peng Hsu

Abstract:

This paper adopts a two-stage data envelopment analysis to explore the impacts of financial development and bank operating scale on bank efficiencies. The sample comprises unbalanced panel data of 32 Taiwanese listed domestic commercial banks over the period 1998 to 2013. Empirical results show that pure technical efficiency is positively related to financial development, whereas the effect of financial development on scale efficiency is insignificant. Enlargement of bank operating scale improves bank efficiencies, but the efficiency gains are decreased gradually when the scale increases. Increases in capital adequacy ratio and market power of loans lead into a growth of bank efficiencies.

Keywords: Financial development, Operating scale, Efficiency, DEA.

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7841 The Model to Calculate the Cost of Money to the Breakdown of Deposits and Banking Service

Authors: Javad Elkaie Behjati, Mehrzad Minouei

Abstract:

The present study aimed to assess the cost of money based on separating deposits and identifying actions and costs affecting in the process of cost of money in EN Bank of Iran (also known as Eghtesad Novin Bank). The method to calculate the cost of money is based on Activity-Based Costing (ABC). To conduct the study, the required data including deposits in banks and absorbed costs related to the same deposits were extracted from the financial statements of the bank. In order to cost the bank services properly as well as determining the commercial strategies required by commercial units, the data are precisely studied and the cost of each deposit is calculated according to the ABC. Eventually, the factors helping to improve the cost management and also a new model to calculate the cost of money in the bank are presented by some applicable formulas. Furthermore, some offers have been provided for users of both sections, in the practical section in commercial units and the theoretical one in universities.

Keywords: The cost of money, activity-based costing, banking, bank deposits, bank fees, services bank.

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7840 Information Seeking through Assimilation Process in Thai Organization

Authors: Pornprom Chomngam

Abstract:

The purpose of this study is to examine employee assessments of the usefulness/value of different types of information available to those employees during the process of organizational assimilation. Participants in the study were 247 “new" employees at Bangkok Bank. Bangkok Bank considers employees whose length of stay with the bank has been less than 18 months as new employees. Questionnaires were administered to all of the Bank-s new employees to obtain the data for this study. Repeated measures analysis was used to analyze the data. The data were summed and coded by using Statistical Package for Social Science. Newcomers indicate that social information is the most useful information, followed by job (technical, referent, and appraisal information), political, normative, and organizational information. Essentially, social, job, and political information are evaluated by newcomers as highly useful, while normative and organizational information are rated as moderately useful.

Keywords: Information seeking, organization assimilation.

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7839 An Investigation of Customers’ Perception and Attitude towards Krung Thai Bank in Thailand

Authors: Phatthanan Chaiyabut

Abstract:

The purposes of this research were to identify the perception of customers towards Krung Thai Bank’s image and to understand the customer attitude towards Krung Thai Bank’s image in Bangkok, Thailand. This research utilized quantitative approach and used questionnaire as data collection tool. A sample size of 420 respondents was selected by simple random sampling. The findings revealed that the majority of respondents received information, news, and feeds concerning the bank through televisions the most. This information channel had significantly influenced on the customers and their decisions to utilize the bank’s products and services.

From the information concerning the attitudes towards overall image of the bank, it was found that the majority respondents rated the bank’s image at the good level. The top three average attitudes included the bank’s images in supports government's monetary policies, being renowned and stable, and contributing in economical amendments and developments, with the mean average of 4.01, 3.96 and 3.81 respectively. The attitudes toward the images included a business leader in banking, marketing, and competitions. Offering prompt services, and provided appropriate servicing time were rated moderate with the attitudes of 3.36 and 3.30 respectively.

Keywords: Attitude, Image, Krung Thai bank, Perception.

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7838 Parallezation Protein Sequence Similarity Algorithms using Remote Method Interface

Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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7837 Banks Profitability Indicators in CEE Countries

Authors: I. Erins, J. Erina

Abstract:

The aim of the present article is to determine the impact of the external and internal factors of bank performance on the profitability indicators of the CEE countries banks in the period from 2006 to 2012. On the basis of research conducted abroad on bank and macroeconomic profitability indicators, in order to obtain research results, the authors evaluated return on average assets (ROAA) and return on average equity (ROAE) indicators of the CEE countries banks. The authors analyzed profitability indicators of banks using descriptive methods, SPSS data analysis methods, as well as data correlation and linear regression analysis. The authors concluded that most internal and external indicators of bank performance have no direct influence the profitability of the banks in the CEE countries. The only exceptions are credit risk and bank size, which affect one of the measures of bank profitability – return on average equity.

Keywords: Banks, CEE countries, Profitability ROAA, ROAE.

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7836 Bank Loans and the Business Cycle: The Case of the Czech Republic

Authors: Libena Cernohorska, Jan Cernohorsky

Abstract:

This article aims to evaluate the impact of loans provided within the Czech banking sector on the growth of the Czech economy. The article is based on research of current scientific findings in respect to bank loans and economic development. The paper is based on data taken from the Czech Statistical Office on the development of the gross domestic product and data from the Czech National Bank on the development of loans from the period 2004-2015. Links between selected variables are tested using Granger causality tests. The results calculated confirm the hypothesis of the impact of the loans on economic growth, with a six-month delay. The results thus correspond to the standard economic findings and results of most previous studies.

Keywords: Bank, business cycle, economic growth, loans.

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7835 Influence of Locus of Control and Job Involvement to Organizational Culture Applied by Employees on Bank X

Authors: Sri Suwarsi, Nadia Budianti

Abstract:

As one of the big government bank, Bank X is paying attention its performance, so that it can compete. One of them is the existence of organizational culture which recognized with term TIPEC (Trust, Integrity, Professionalism, Costumer Focus, and Excellence). In application of organizational culture, it is needed the existence of employee involvement (job involvement). It can be influenced by various factors, such as Locus of Control. Related to above mentioned, the problems are how employee tendency of Locus of Control, how job involvement, how organizational culture applied by employees and how influence of Locus of Control and job involvement to the organizational culture applied by employees. Researchers collected data with questioner spreading, and respondents number of 30 people. After that, the data were analyzed with SPSS software constructively. The influence of Locus of Control and job involvement to the application of organizational culture was strong, i.e. 58.3%.

Keywords: Organizational culture, bank, employee locus of control, job involvement.

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7834 Development of Monitoring Blood Bank Center Based PIC Microcontroller Using CAN Communication

Authors: Kaiwan S. Ismael, Ergun Ercelebi, Majeed Nader

Abstract:

This paper describes the design and implementation of a hardware setup for online monitoring of 24 refrigerators inside blood bank center using the microcontroller and CAN bus for communications between each node. Due to the security of locations in the blood bank hall and difficulty of monitoring of each refrigerator separately, this work proposes a solution to monitor all the blood bank refrigerators in one location. CAN-bus system is used because it has many applications and advantages, especially for this system due to easy in use, low cost, providing a reduction in wiring, fast to repair and easily expanding the project without a problem.

Keywords: Control Area Network (CAN), monitoring blood bank center, PIC microcontroller, MPLAB IDE.

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7833 Predicting the Success of Bank Telemarketing Using Artificial Neural Network

Authors: Mokrane Selma

Abstract:

The shift towards decision making (DM) based on artificial intelligence (AI) techniques will change the way in which consumer markets and our societies function. Through AI, predictive analytics is being used by businesses to identify these patterns and major trends with the objective to improve the DM and influence future business outcomes. This paper proposes an Artificial Neural Network (ANN) approach to predict the success of telemarketing calls for selling bank long-term deposits. To validate the proposed model, we uses the bank marketing data of 41188 phone calls. The ANN attains 98.93% of accuracy which outperforms other conventional classifiers and confirms that it is credible and valuable approach for telemarketing campaign managers.

Keywords: Bank telemarketing, prediction, decision making, artificial intelligence, artificial neural network.

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7832 A Bayesian Kernel for the Prediction of Protein- Protein Interactions

Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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7831 ATM Service Analysis Using Predictive Data Mining

Authors: S. Madhavi, S. Abirami, C. Bharathi, B. Ekambaram, T. Krishna Sankar, A. Nattudurai, N. Vijayarangan

Abstract:

The high utilization rate of Automated Teller Machine (ATM) has inevitably caused the phenomena of waiting for a long time in the queue. This in turn has increased the out of stock situations. The ATM utilization helps to determine the usage level and states the necessity of the ATM based on the utilization of the ATM system. The time in which the ATM used more frequently (peak time) and based on the predicted solution the necessary actions are taken by the bank management. The analysis can be done by using the concept of Data Mining and the major part are analyzed based on the predictive data mining. The results are predicted from the historical data (past data) and track the relevant solution which is required. Weka tool is used for the analysis of data based on predictive data mining.

Keywords: ATM, Bank Management, Data Mining, Historical data, Predictive Data Mining, Weka tool.

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7830 Bank Business Models and The Changes in CEE Countries

Authors: I. Erins, J. Erina

Abstract:

The aim of this article is to assess the existing business models used by the banks operating in the CEE countries in the time period from 2006 till 2011. In order to obtain research results, the authors performed qualitative analysis of the scientific literature on bank business models, which have been grouped into clusters that consist of such components as: 1) capital and reserves; 2) assets; 3) deposits, and 4) loans. In their turn, bank business models have been developed based on the types of core activities of the banks, and have been divided into four groups: Wholesale, Investment, Retail and Universal Banks. Descriptive statistics have been used to analyse the models, determining mean, minimal and maximal values of constituent cluster components, as well as standard deviation. The analysis of the data is based on such bank variable indices as Return on Assets (ROA) and Return on Equity (ROE).

Keywords: Banks, Business model, CEE, ROA, ROE.

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7829 Determination of the Bank's Customer Risk Profile: Data Mining Applications

Authors: Taner Ersoz, Filiz Ersoz, Seyma Ozbilge

Abstract:

In this study, the clients who applied to a bank branch for loan were analyzed through data mining. The study was composed of the information such as amounts of loans received by personal and SME clients working with the bank branch, installment numbers, number of delays in loan installments, payments available in other banks and number of banks to which they are in debt between 2010 and 2013. The client risk profile was examined through Classification and Regression Tree (CART) analysis, one of the decision tree classification methods. At the end of the study, 5 different types of customers have been determined on the decision tree. The classification of these types of customers has been created with the rating of those posing a risk for the bank branch and the customers have been classified according to the risk ratings.

Keywords: Client classification, loan suitability, risk rating, CART analysis, decision tree.

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7828 A Decision Support Model for Bank Branch Location Selection

Authors: Nihan Cinar

Abstract:

Location selection is one of the most important decision making process which requires to consider several criteria based on the mission and the strategy. This study-s object is to provide a decision support model in order to help the bank selecting the most appropriate location for a bank-s branch considering a case study in Turkey. The object of the bank is to select the most appropriate city for opening a branch among six alternatives in the South-Eastern of Turkey. The model in this study was consisted of five main criteria which are Demographic, Socio-Economic, Sectoral Employment, Banking and Trade Potential and twenty one subcriteria which represent the bank-s mission and strategy. Because of the multi-criteria structure of the problem and the fuzziness in the comparisons of the criteria, fuzzy AHP is used and for the ranking of the alternatives, TOPSIS method is used.

Keywords: MCDM, bank branch location, fuzzy AHP, TOPSIS.

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7827 Analysis of Formyl Peptide Receptor 1 Protein Value as an Indicator of Neutrophil Chemotaxis Dysfunction in Aggressive Periodontitis

Authors: Prajna Metta, Yanti Rusyanti, Nunung Rusminah, Bremmy Laksono

Abstract:

The decrease of neutrophil chemotaxis function may cause increased susceptibility to aggressive periodontitis (AP). Neutrophil chemotaxis is affected by formyl peptide receptor 1 (FPR1), which when activated will respond to bacterial chemotactic peptide formyl methionyl leusyl phenylalanine (FMLP). FPR1 protein value is decreased in response to a wide number of inflammatory stimuli in AP patients. This study was aimed to assess the alteration of FPR1 protein value in AP patients and if FPR1 protein value could be used as an indicator of neutrophil chemotaxis dysfunction in AP. This is a case control study with 20 AP patients and 20 control subjects. Three milliliters of peripheral blood were drawn and analyzed for FPR1 protein value with ELISA. The data were statistically analyzed with Mann-Whitney test (p>0,05). Results showed that the mean value of FPR1 protein value in AP group is 0,353 pg/mL (0,11 to 1,18 pg/mL) and the mean value of FPR1 protein value in control group is 0,296 pg/mL (0,05 to 0,88 pg/mL). P value 0,787 > 0,05 suggested that there is no significant difference of FPR1 protein value in both groups. The present study suggests that FPR1 protein value has no significance alteration in AP patients and could not be used as an indicator of neutrophil chemotaxis dysfunction.

Keywords: Aggressive periodontitis, chemotaxis dysfunction, FPR1 protein value, neutrophil.

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7826 Owner/Managers’ External Financing Used and Preference towards Islamic Banking

Authors: Khalid Hassan Abdesamed, Kalsom Abd Wahab

Abstract:

Economic development and growth are significantly linked to the consistent and sustainable sector of small and medium enterprises (SMEs). Banks are the frontrunners in financing and advising SMEs. The main objective of the study is to assess the tendency of SMEs to use the Islamic bank. Model was developed using quantitative method with a hypothetical-deductive testing approach. Model (N = 364) used primary data on the tendency of SMEs to use Islamic banks gathered from questionnaire. It is found by Mann-Whitney test that the tendency to use Islamic bank varies between those firms which consider formal financing with the ones relying on informal financing with the latter tends more to use Islamic bank. This study can serve academic researchers, policy makers, and developing countries as a model of SMEs’ desirability to Islamic banking.

Keywords: Formal financing, informal financing, Islamic bank, SMEs.

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7825 Critical Assessment of Scoring Schemes for Protein-Protein Docking Predictions

Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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7824 E-Service and the Nigerian Banking Sector: A Review of ATM Architecture and Operations

Authors: Bashir A. Yauri, Aliyu R. Yauri

Abstract:

With the introduction of cash-less society policy by the Central Bank of Nigeria, the concept of e-banking services have over the years’ experience a significant improvement. Today quite a number of people are embracing e-banking activities especially ATM, thereby moving away from the conventional banking system. This paper presents a review of the underlying Architectural Layout of Intra-Bank and Inter-Bank ATM connectivity in Nigeria. The paper further investigates and discusses factors affecting the Intra- Bank and Inter-Bank ATM connectivity in Nigeria. In addition, as well possible solutions to these factors affecting ATM Connectivity and Operations are proposed.

Keywords: Architectural layout, automated teller machine, e-services, interswitch.

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7823 Correspondence between Function and Interaction in Protein Interaction Network of Saccaromyces cerevisiae

Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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7822 One-Class Support Vector Machines for Protein-Protein Interactions Prediction

Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.

Keywords: Bioinformatics, Protein-protein interactions, One-Class Support Vector Machines

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7821 Comparison of Domain and Hydrophobicity Features for the Prediction of Protein-Protein Interactions using Support Vector Machines

Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.

Keywords: Bioinformatics, protein-protein interactions, support vector machines, protein features.

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7820 Predicting Protein Function using Decision Tree

Authors: Manpreet Singh, Parminder Kaur Wadhwa, Surinder Kaur

Abstract:

The drug discovery process starts with protein identification because proteins are responsible for many functions required for maintenance of life. Protein identification further needs determination of protein function. Proposed method develops a classifier for human protein function prediction. The model uses decision tree for classification process. The protein function is predicted on the basis of matched sequence derived features per each protein function. The research work includes the development of a tool which determines sequence derived features by analyzing different parameters. The other sequence derived features are determined using various web based tools.

Keywords: Sequence Derived Features, decision tree.

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7819 Selecting Negative Examples for Protein-Protein Interaction

Authors: Mohammad Shoyaib, M. Abdullah-Al-Wadud, Oksam Chae

Abstract:

Proteomics is one of the largest areas of research for bioinformatics and medical science. An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. Predicting Protein-Protein Interaction (PPI) is one of the crucial and decisive problems in current research. Genomic data offer a great opportunity and at the same time a lot of challenges for the identification of these interactions. Many methods have already been proposed in this regard. In case of in-silico identification, most of the methods require both positive and negative examples of protein interaction and the perfection of these examples are very much crucial for the final prediction accuracy. Positive examples are relatively easy to obtain from well known databases. But the generation of negative examples is not a trivial task. Current PPI identification methods generate negative examples based on some assumptions, which are likely to affect their prediction accuracy. Hence, if more reliable negative examples are used, the PPI prediction methods may achieve even more accuracy. Focusing on this issue, a graph based negative example generation method is proposed, which is simple and more accurate than the existing approaches. An interaction graph of the protein sequences is created. The basic assumption is that the longer the shortest path between two protein-sequences in the interaction graph, the less is the possibility of their interaction. A well established PPI detection algorithm is employed with our negative examples and in most cases it increases the accuracy more than 10% in comparison with the negative pair selection method in that paper.

Keywords: Interaction graph, Negative training data, Protein-Protein interaction, Support vector machine.

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7818 Protein Residue Contact Prediction using Support Vector Machine

Authors: Chan Weng Howe, Mohd Saberi Mohamad

Abstract:

Protein residue contact map is a compact representation of secondary structure of protein. Due to the information hold in the contact map, attentions from researchers in related field were drawn and plenty of works have been done throughout the past decade. Artificial intelligence approaches have been widely adapted in related works such as neural networks, genetic programming, and Hidden Markov model as well as support vector machine. However, the performance of the prediction was not generalized which probably depends on the data used to train and generate the prediction model. This situation shown the importance of the features or information used in affecting the prediction performance. In this research, support vector machine was used to predict protein residue contact map on different combination of features in order to show and analyze the effectiveness of the features.

Keywords: contact map, protein residue contact, support vector machine, protein structure prediction

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7817 Dynamic Shock Bank Liquidity Analysis

Authors: C. Recommandé, J.C. Blind, A. Clavel, R. Gourichon, V. Le Gal

Abstract:

Simulations are developed in this paper with usual DSGE model equations. The model is based on simplified version of Smets-Wouters equations in use at European Central Bank which implies 10 macro-economic variables: consumption, investment, wages, inflation, capital stock, interest rates, production, capital accumulation, labour and credit rate, and allows take into consideration the banking system. Throughout the simulations, this model will be used to evaluate the impact of rate shocks recounting the actions of the European Central Bank during 2008.

Keywords: CC-LM, Central Bank, DSGE, Liquidity Shock, Non-standard Intervention.

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7816 Optimization of Protein Hydrolysate Production Process from Jatropha curcas Cake

Authors: Waraporn Apiwatanapiwat, Pilanee Vaithanomsat, Phanu Somkliang, Taweesiri Malapant

Abstract:

This was the first document revealing the investigation of protein hydrolysate production optimization from J. curcas cake. Proximate analysis of raw material showed 18.98% protein, 5.31% ash, 8.52% moisture and 12.18% lipid. The appropriate protein hydrolysate production process began with grinding the J. curcas cake into small pieces. Then it was suspended in 2.5% sodium hydroxide solution with ratio between solution/ J. curcas cake at 80:1 (v/w). The hydrolysis reaction was controlled at temperature 50 °C in water bath for 45 minutes. After that, the supernatant (protein hydrolysate) was separated using centrifuge at 8000g for 30 minutes. The maximum yield of resulting protein hydrolysate was 73.27 % with 7.34% moisture, 71.69% total protein, 7.12% lipid, 2.49% ash. The product was also capable of well dissolving in water.

Keywords: Production, protein hydrolysate, Jatropha curcas cake, optimization.

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