Inquiry (E-Journal - Faculty of Business and Administration, International University of Sarajevo)
Not a member yet
209 research outputs found
Sort by
A Computational Biology Approach in Function Annotation to Enzymes
No full textAlthough homologous proteins do not necessarily exhibitidentical biochemical functions, local and global sequence similarity is widely used as an indication of functional identity. Enzyme Commission (EC) classified hundreds of thousands of enzymes into six essential classes. Then in each class, enzymes are given four digits numbers such that enzymes with identical functions carry the same EC number. EC numbers provide a well-defined, non-ambiguous method for annotation of enzyme function. In this article, in each of six enzyme class, enzymes are classified according to their EC numbers into enzyme subclasses. Among enzymes and enzyme subclasses a new similarity measure is defined, and it is seen that, similar enzymes according to this new similarity measure exhibit identical biochemical functions in 94% of the cases. This similarity measure is used for function annotation to enzymes, and an average accuracy rate of 94% is achieved. The technique is also used for function annotation to unknown enzymes
Recurrent Neural Networks for Linear B-Epitope Prediction in Antigens
No full textExperimental methods used for characterizing epitopes that play a vital role in the development of peptide vaccines, in diagnosis of diseases, and also for allergy research are time consuming and need huge resources. There are many online epitope prediction tools that can help experimenters in short listing the candidate peptides. To predict B-cell epitopes in an antigenic sequence, Jordan recurrent neural network (JRNN) are found to be more successful. To train and test neural networks, 262.583 B epitopes are retrieved from IEDB database. 99.9% of these epitopes have lengths in the interval 6-25 amino acids. For each of these lengths, committees of 11 expert recurrent neural networks are trained. To train these experts alongside epitopes, non-epitopes are needed. Non-epitopes are created as random sequences of amino acids of the same length followed by a filtering process. To distinguish epitopes and non-epitopes, the votes of eleven experts are aggregated by majority vote. An overall accuracy of 97.23% is achieved. Then these experts are used to predict the linear b epitopes of antigen, ESAT6 (Tuberculosis)
Validation Tools for Predicted Linear B-Epitopes: Surface Flexibility
No full textProtein structural flexibility is important for catalysis, and binding. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. Karplus, and Shultz divided amino acids in two categories, rigid and flexible. Then, proposed three flexibility scales for residues with no rigid neighbors, residues with one rigid neighbor, and residues for which both neighbors are rigid. To use flexibility scores for validation of candidate b-epitopes, 337,259 b-epitopes whose lengths are larger than seven amino acids are downloaded from iedb database, and 103,590 non epitopes are created randomly. When computed by Karplus-Shultz technique, b-epitopes achieved an average score of 1.0159, while the average score for non epitops is 0.9752. It is seen that the Karplus, and Shultz flexibility computation technique can be used as a validation tool with the criteria that the peptide with higher score, is more likely an epitope
Computational Geometry Applications
Get PDFComputational geometry is an integral part of mathematics and computer science deals with the algorithmic solution of geometry problems. From the beginning to today, computer geometry links different areas of science and techniques, such as the theory of algorithms, combinatorial and Euclidean geometry, but including data structures and optimization. Today, computational geometry has a great deal of application in computer graphics, geometric modeling, computer vision, and geodesic path, motion planning and parallel computing. The complex calculations and theories in the field of geometry are long time studied and developed, but from the aspect of application in modern information technologies they still are in the beginning. In this research is given the applications of computational geometry in polygon triangulation, manufacturing of objects with molds, point location, and robot motion planning
Inferring Protein Function from Structure
Get PDFA major goal of molecular biology is to understand functions of all genes in nature. Accordingly, it is of great importance to improve large-scale functional genomics and proteomics experiments. However, due to costly and time-consuming nature of experiments, bioinformatics approach to infer the function appears to be very attractive. Besides this, there are many proteins of known structure which are not yet functionally characterized. This makes the investigation of sequence-function and structure-function relationships even more necessary. The number of methods for in silico annotation of function has increased enormously over the past few decades, from methods that rely on high sequence similarity between a protein of unknown function and a family of well-characterized proteins to methods that rely on "profiles" to infer the function. Although computational approach of inferring protein function is an important challenge, there are many obstacles to overcome. First, a function is not well defined and can be defined at several levels of detail. Accordingly, it is very difficult to create controlled vocabularies. Second, the precise values for thresholds of significant sequence similarity are actually specific to particular aspects of function and have to be re-established for any given task. The most common approach to study the function is through evolutionary relationship, or homology, with proteins of known function and it is based on the assumptions that "homologous proteins that have similar sequences and structures, have similar functions" which is the so called Sequence-Structure-Function Paradigm. In this research project, the limitations of this approach are studied
Validation Tools for Predicted Linear B-Epitopes: Beta Turns
No full textIt is claimed that amino acid replacements in surface loops usually do not perturb the three-dimensional structure of the protein, since surface loops are relatively flexible (Saunders and Baker 2002). Thus, the conservation variability of epitopes might be biased by the abundance of loops in epitopes. These results imply that epitopes do not tend to overlap functional regions, but rather cover separate regions. Pellequera, et. al., (1993), developed new turn scales based on the occurrence of amino acids at each of the four positions of a turn using a structural database comprised of 87 proteins. It is found that the scales correctly predicted a fraction of the turn regions in proteins with approximately 80% confidence. They used the turn scales for predicting the location of antigenic sites in proteins. The method was developed with the specific aim of predicting only a few peaks for each protein. They found that it leads to a high level of accurate prediction around 70% of correct prediction of known epitopes. In this article we update turn scales using large numbers of proteins and epitopes. Improved method will be more helpful in selecting protein regions to be synthesized in order to produce anti-peptide antibodies cross-reacting with the parent protein
Hydrophilicity of Linear B-Epitopes
Get PDFAntigenic sites of a protein are those recognized by antibodies. Therefore it is most likely that these sites are accessible or on the surface of the protein, and these regions are probably more mobile than interior regions. Since these sites are on the surface, they are probably hydrophilic. Indeed, algorithms for hydrophilicity and accessibility have been used to predict antigenicity. In this research, the hydrophilicity by Parker’s scale, and hydrophobicityby Cornette, and Doolittle scales of linear b-rpitopes is studied on 344121 linear b-eptopes downloaded from iedb epitope database. Descriptive statistical analyses revealed that average hydrophilicity of these b-epitopes distributes normally with mean =2.1993, standard deviation σ=1.9303, skewness s= - 0.2681, and kurtosis =3.1826. It is seen that mean hydrophobicities are also distribute normally. A detailed review is performed to scan available hydrophophilicity/hydrophobicity scales. Altogether 24 scales are listed
A Recurrent Neural Network Linear B-Epitope Predictor: BIRUNI
No full textExperimental methods used for characterizing epitopes that play a vital role in the development of peptide vaccines, in diagnosis of diseases, and also for allergy research are time consuming and need huge resources. There are many online epitope prediction tools are available that can help scientists in short listing the candidate peptides. To predict B-cell epitopes in an antigenic sequence, Jordan recurrent neural network (BIRUNI) is found to besuccessful. To train and test neural networks, 262.583 B epitopes are retrieved from IEDB database. 99.9% of these epitopes have lengths in the interval 6-25 amino acids. For each of these lengths, committees of 11 expert recurrent neural networks are trained. To train these experts alongside epitopes, non-epitopes are needed. Non-epitopes are created as random sequences of amino acids of the same length followed by a filtering process. To distinguish epitopes and non-epitopes, the votes of eleven experts are aggregated by majority vote. An overall accuracy of 97.23% is achieved. Then these experts are used to predict the Linear Bepitopes of five antigens, Plasmodium Falciparum, Human Polio Virus Sabin Strain, Meningitis, Plasmodium Vivax and Mycobacterium Tuberculosis. The success of BIRUNU is compared with the five online prediction tools ABCPRED, BCPRED, K&T, BEPIPRED, and AAP.It is seen that BIRUNI outperforms all of them in the average
The Significance of Using Ict in Telemetric Monitoring, Process Weighing and Control of The Coal
No full textThe aim of this article is to present the indicators that affect the technical feasibility and economic justification of investment in ICT infrastructure and information systems. We performed this task by reviewing the specific case study "Construction of computer networks and information systems for weighing and control of coal in RMU Banovići". The article presents the technical aspects of implementation and operation of such projects and the potential savings as well as the ability for a better control of the revenue side of the company, which brings better results for business and competitiveness in the market economy
A Mixed Integer Linear Programming Model for End of Life Vehicles Recycling Network Design
Get PDFAutomotive industry, with both its contributions to the technology and values added to the economy, has been indisputably one of the leading sectors. As the demand and interest in automobile grow, the environmental pollution caused by the automobiles increases correspondingly. In addition to automobiles’ carbon emissions, also the vehicles which have completed their life cycle, namely scrap vehicles, cause environmental pollution due to their solid and liquid waste. In developed countries, a regulation has been made in order to prevent the situation from getting worse. According to this regulation, in order to support product management, manufacturers are obliged to take back and recycle all their vehicles which have completed their life cycle. The regulation started to be implemented after being adapted to the national law. Upon its adaptation to our national regulations, it has been enforced in our country as well.
In the study, Mixed Integer Linear Programming (MILP) model has been presented to design end of life vehicles recycling network. The proposed model has minimized the total network cost as well as to determine the amount of material transported between the facilities and to decide whether to open the dismantling and shredding facilities. The presented model has been applied to end of life vehicles recycling network design problem in Istanbul. The proposed model gives suitable and cost effective results for end of life vehicles recycling network in Istanbul