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In recent years, billions of DNA and protein sequences are subject to sequencing. However, few of them have known structures and functions, most remain unknown. The solution to this problem is to link sequences between them rather than revisit each new sequence independently of other sequences. Thus, if we manage to assimilate a sequence S1 to another sequence S2 or to a group of previously studied...
With the constant increase in the number and variety of small molecule chemical compounds, drug discovery is becoming a very resource intensive endeavor. Performing molecular simulations of ligand-protein binding by virtual screening has become an integral part of the discovery process. Cloud computing is an efficient choice to execute these large-scale screenings, given that large compute allocations...
Food Consumption Patterns will be very important to regulate human nutrition. With good and organized food consumption patterns all the nutritional needs can be fullfilled. An unorganized food consumption patterns can lead to lack of nutritional needs‥ Besides, it will cause disease. The problems that occurred in Indonesia are still many people who lack awareness about good food consumption patterns,...
As the first cancer-causing human virus identified, Epstein-Barr virus (EBV) has been implicated in the development of a wide range of B cell lymphoproliferative disorders, a subset of T/NK cell lymphomas, and post-transplant lymphoproliferative disorders. We made use of the immunological data on EBV available through publications, technical reports, and databases and constructed Epstein-Barr virus...
The 2014 Ebola outbreak in West Africa raised global concern requiring concerted effort from the worldwide scientific community to analyze immune responses, in natural infection and in the context of vaccination and therapy. Herein we review and analyze antibody and T cell epitope data reported in the scientific literature. More than 100 epitopes have been defined for viruses within the Filoviridae...
The widespread use of mass spectrometry for protein identification has created an urgent demand for improving computational efficiency of matching mass spectrometry data to protein databases. With the rapid development of chip technology and parallel computing technique, such as multi-core processor, many-core coprocessor and cluster of multi-node, the speed and performance of the major mass spectral...
At the center of computational structural biology, protein structure comparison is a key problem. The steady increase in the number of protein structures encourages the development of massively parallel tools. While the focus of research is to propose data-analytical methods to tackle this problem, there are limited research proposing generic tools to run these methods in parallel environments. Herein,...
Knowledge discovery in genomics involves large scale graph processing and inference which is different from high-performance computing in genomics for sequence analysis. Genomics datasets are becoming increasing large and varied due to advances in biotechnology. Traditional sequence analysis therefore is computation-intensive for tasks such as assembly of reads, mapping reads to genomes, variation...
Due to the fact that proper dietary planning will maintain the healthiness of patients, plus a food consumption control is an important clinical treatment of certain diseases of medical healthcare. This paper is aimed at proposing a practical solution to generate an automated schedule for both the In- Patient Department (IPD) and Out-Patient department (OPD) for a hospital. The challenges of this...
Computational drug designing represents a new approach towards drug discovery. In this study, structure based drug design was used to find an antibiofilm agent to suppress Pseudomonas aeruginosa biofilm production in venous catheters and artificial hip prosthesis. PelD protein was chosen as a target protein for this process as it dominates exopolysaccharide matrix formation and compactness of biofilm...
Fusarium circinatum is a disease-causing fungal agent responsible for pitch canker disease in pine trees. In this study, the cytochrome b protein which plays an important role in electron transport chain for respiration is taken as a crucial target for developing anti-fungal inhibitors. We predicted the protein model of cytochrome b in Fusarium circinatum based on the Saccharomyces cytochrome b template...
The Smith-Waterman local alignment algorithm is the method of choice for protein database searches because it is often able to detect remote homologues for a query protein sequence. However, it is also well known that the reliability of this algorithm degrades sharply for proteins with low similarity to a given query — so-called "twilight zone" matches. In these situations, global alignments...
In this paper, we develop a new technique to store, search and compare DNA sequences. We utilize the concept of multiwindow Gabor representations and use these functions to handle the nucleotide sequences. We show specifically, that using multiwindow Gabor representations, it is possible to represent the sequences efficiently using very few terms. Further, we develop a search technique based on the...
The problem of inferring proteins from complex peptide samples in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing throughputs, rapid processing rates and reliability of results. This is exacerbated by the fact that, in general, a given protein cannot be defined by a fixed sequence of amino acids due to the existence of splice...
Childhood is a dynamic period of life that rapid growth and development take place. Making mistakes in feeding practices of children may lead to undesirable consequences like malnutrition and obesity. Use of an automated computer-based technique to assist determination of daily dietary requirements of energy, protein and water has potential for preventing malnutrition and obesity. To get the solution...
As biological databases are growing in terms of numbers, size and complexity, managing these databases is becoming very complex. Most of these databases emerged as the output of experimental research by scientists. However, many of the scientists were not trained on the informatics side of research and also there were few standards available to be followed in defining these databases. This resulted...
We propose a method for automatically determining the amount of each ingredient used to prepare a commercial food using the information provided on its label. The method applies when no part of any ingredient is removed in the preparation process and as long as we can collect the nutrition data (e.g., from the USDA Food Database) for at least some of the ingredients. Using this information, we first...
In this paper we consider the application of machine learning of graphical models and feature selection for developing better drug-design strategies. The work discussed in this paper is based on utilizing partial prior knowledge available through KEGG signalling pathway database in tan dim with our recent developed ensemble feature selection methods for a better regularisation of the lasso estimate...
Intrinsically disorder regions (IDRs) or, proteins (IDPs) are associated with important biological functions, while lacking stable structure in their native state. The phenomena of disordered proteins or residues are abundant in nature and are extensively involved in critical human diseases and hence impacting drug discovery. Thus, the study using disorder prediction is becoming crucial in the proteomic...
In the fields of bioinformatics and drug discovery, prediction of bacterial proteins is an important research. We proposed a novel classifier ensemble scheme for the prediction of Gram-positive bacterial protein. The proposed methodology exploits diversity in decision space through different machine learning techniques. However, diversity in feature spaces is exploited using physicochemical properties...
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