Journal of
Computational Biology and Bioinformatics Research

  • Abbreviation: J. Comput. Biol. Bioinform. Res
  • Language: English
  • ISSN: 2141-2227
  • DOI: 10.5897/JCBBR
  • Start Year: 2009

JCBBR Articles

October 2018

Theoretical and conceptual derivation of threshold phenomena and metabolic switching models in a chemostat system

A chemostat cell culture is a polyphasic dispersed system. Three models using net transport and metabolization (T/M) kinetics of hyperbolic form have been described. The first uses only one metabolic pathway and has been studied under various conditions. The second uses two metabolic pathways, with either high or low affinity for the substrate. The third adds excretion of fermentative products to the pathways in model...

Author(s): Jacques Thierie  

May 2018

Selection of T cell epitopes from S. mansoni Sm23 protein as a vaccine construct, using Immunoinformatics approach

Schistosomiasis, a neglected and most prevalenttropical diseases after malaria, have been a threat to people living in endemic areas. With regards to possible resistance to the popular drug (praziquantel) use for treatment of schistosomiasis, the need for a permanent vaccinating approach has been justified. This study uses an in silico approach to identify potential target vaccine candidate or T cell epitopes (T cell...

Author(s): Onile Olugbenga Samson, Fadare Shadrach Olaleka and Omitogun G. Ofelia,

May 2015

Computational sequence analysis and in silico modeling of a stripe rust resistance protein encoded by wheat TaHSC70 gene

TaHSC70 gene of Triticum sp. is an associate of the heat shock protein family and plays a significant role in stress-related and defense responses educed by contagion with stripe rust fungus through a Jasmonic acid dependent signal transduction pathway. Hence, understanding molecular structure and function of the protein coded by this gene is of paramount importance for plant biologists working on stripe rust. The...

Author(s): Zarrin Basharat

November 2014

Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms

Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate within more complex multi-SNP haploblocks that are maintained throughout generations in a stable population. Information encoded in the structure of SNPs and SNP haploblock variation can be characterized through a normalized information content metric. Genodynamics is...

Author(s): James Lindesay, Tshela E Mason, William Hercules and Georgia M Dunston,

July 2013

Does a protein coevolve with its multiple interacting partners? A case study

Protein-protein interactions are playing a fundamental role in different cellular activities.  Although the coevolution of interacting protein pairs has been established by several groups, whether a protein having multiple interacting partners coevolves with all of its interacting partners or not have not been studied, so far. Here, the coevolution of proliferating cell nuclear antigen (PCNA) with their multiple...

Author(s): Subinoy Biswas and Sudip Kundu

April 2013

MLH1 gene: An in silico analysis

The MLH1 gene responsible for colon cancer has been examined to identify functional consequences of single-nucleotide polymorphisms (SNPs). 16 SNPs have been identified in the MLH1 gene in which all are found to be nonsynonymous. Non synymous SNPs are relevant in many of the human inherited diseases since they change the aminoacid sequence of the protein. 56% of the identified nsSNPs have been reported as damaging. In...

Author(s): Amitha Joy, Jubil, C. A, Syama, P. S and Rohini Menon

April 2013

Annotation of virulence factors in schistosomes for the development of a SchistoVir database

Scientific efforts in the eradication of neglected tropical diseases, such as those caused by the parasitic helminthes, can be improved if a database of key virulence factors directly implicated in pathogenesis is available. As a first step towards creating SchistoVir, a database of virulence protein factors in schistosomes, in this study, we curated, annotated and aligned sequences of twenty virulence factors...

Author(s): Adewale S. Adebayo and Chiaka I. Anumudu

December 2012

Establishment of rice yield prediction model using canopy reflectance

The major objectives of this study were to identify spectral characteristics associated with rice yield and to establish their quantitative relationships. Field experiments were conducted at Shi-Ko experimental farm of TARI’s Chiayi Station, during 2001 to 2005. Rice cultivar Tainung 67 (Oryza sativa L.), the major cultivar grown in Taiwan, was used in the study. Various levels of rice yield were obtained via...

Author(s): K. W. Chang

December 2012

Three dimensional modelling of beta endorphin and its interaction with three opioid receptors

Beta endorphin is a neurotransmitter and is involved in functions like enhancement of immune system, deceleration of cancer cell growth and induction of euphoria and relaxation. It is an opioid like neuropeptide synthesized in neurons of hypothalamus and pituitary gland. The study of its structure and its interaction with opioid receptors can throw light on its neuropsychopharmacology. Protein data bank does not contain...

Author(s): Swathi Aluri and Ramana Terli

April 2012

Analysis of structurally conserved atomic interactions in structural homologs of nicotinamide adenine dinucleotide binding dehydrogenases

The stability of protein-ligand complex is decided by the strength of the forces and interaction that holds the overall structure. The binding of ligand to its receptor involves the participation of atomic interactions of key conserved amino acid residues which are essential for functional and structural integrity of protein molecule. Understanding the binding mechanism of ligand to its receptors is important in...

Author(s): P. S. Solanki, M. Krishna Mohan, P. Ghosh and S. L. Kothari

April 2012

A computational analysis to understand the role of DmsD in the biosynthesis of dimethyl sulfoxide (DMSO) reductase

The role of DmsD in the biosynthesis of dimethyl sulfoxide (DMSO) reductase is quite controversial. Several studies have indicated its role as ‘proof-reading chaperone’, which might function to prevent the translocation of misfolded and non-cofactor containing protein. DmsD is also shown to bind to the signal peptide; however, its possible function as a ‘guidance factor’ for membrane targeting is...

Author(s): Nazlee Sharmin

February 2012

A new biophysical metric for interrogating the information content in human genome sequence variation: Proof of concept

The 21st century emergence of genomic medicine is shifting the paradigm in biomedical science from the population phenotype to the individual genotype. In characterizing the biology of disease and health disparities in population genetics, human populations are often defined by the most common alleles in the group. This definition poses difficulties when categorizing individuals in the population who do not have...

Author(s): James Lindesay, Tshela E. Mason, Luisel Ricks-Santi, William Hercules, Philip Kurianand Georgia M Dunston,

February 2012

Potential of mangrove derived compounds against dihydrofolate reductase: An in-silico docking study

Approximately 3 billion people, one half of the world’s population, live in at-risk regions for malaria infection leading to about 250 million malaria cases every year and nearly one million deaths. Once the malarial parasite Plasmodium vivax and Plasmodium falciparum enters the red blood cells its growth is inhibited by Proguanil, a prophylactic antimalarial drug which inhibits the...

Author(s): Senthilraja P., Sunil Kumar Sahu and Kathiresan K.

January 2012

In silico structure assessment analysis of core domain of six protein data bank entries of HIV-1 Integrase

HIV integrase is a 32 kDa protein produced from the C-terminal portion of the Pol gene product, and is an attractive target for new anti-HIV drugs. Its main function is to insert the viral DNA into the host chromosomal DNA, a step that is essential for its replication. However there are six different Protein Data Bank (PDB) entries of the same protein with the same amino acids with PDB IDs 1BIS, 1BIU, 1BIZ, 1HYV, 1HYZ...

Author(s): Salam Pradeep Singh and B. K. Konwar

January 2012

In silico study of the binding parameters of various antioxidants with human Paraoxonase 1

Paraoxonases are a group of enzymes involved in the hydrolysis of organophosphates. Human Paraoxonase 1 is synthesized in liver and secreted into blood, where it is associated exclusively with High Density Lipoproteins and may protect against the development of atherosclerosis. Paraoxonase was identified as a genetic risk factor for cardiovascular disease. An enhancement of Paraoxonase 1 activity by well-known anti...

Author(s): K. Shyamala, Suhasini Cherine A., Nandha Devi E. and Deepa Gaauthem

December 2011

Bind-Predict: An algorithm for identifying zinc finger binding motifs in DNA sequences

Zinc fingers are the most abundant eukaryotic DNA-binding motifs, which recognize DNA triplets with high efficacy and are used to develop chimeric enzymes for genome modification and site specific gene therapy. Considering the importance of zinc finger motifs and their recognition patterns we have developed a web interface with the incorporation of sequence based search algorithm named as Bind-Predict. This algorithm...

Author(s): Jayaraman Muthukumaran, Mannu Jayakanthan, Sanniyasi Chandrasekar and Premendu P. Mathur

  • Article Number: D44EA679088

December 2011

Nuclear mitochondrial DNA pseudogenes in the genome of the silkworm, Bombyx mori

To understand the types of mitochondrial deoxyribonucleic acid (mtDNA) pseudogenes in the genome of the silkworm Bombyx mori L. (Lepidoptera: Bombycidae) and to determine the origin of the B. mori, the mtDNA of the wild silkworm, Bombyx mandarina Morre was sequenced. Several fragments from the B. mori genome database were obtained with varying degrees of homology toB....

Author(s): Guangli Cao, Renyu Xue, Yuexiong Zhu, Yuhong Wei and Chengliang Gong,

  • Article Number: 93693009115

November 2011

Advancement in computational analysis methods of plant antifreeze proteins (AFPs): An application towards classification and gene expression studies of leucine rich repeat (LRR) and ice-recrystallization inhibition domain (IRI) containing AFPs

Gene sequence analysis is a key-step for genomic research, which help to understand the genome of species once it has been sequenced. It includes pair-wise, comparative or multiple sequence analysis. The Genome On-Line Database (GOLD) provides information about the number of completed, meta, incomplete and targeted genome projects. The statistics of GOLD show 2942 of completed, 7687 of incomplete, 340 of meta...

Author(s): J. Muthukumaran, P. Manivel, M. Kannan, J. Jeyakanthan   and R. Krishna

  • Article Number: E61348B40212

November 2011

Querying formal concepts containing transcription factors: A case study using multiple databases

In order to reduce the amount of information when querying from large databases, one has to develop new approaches. We present here a new way to query our SQUAT database. SQUAT contains formal concepts representing an association between a number of genes that are simultaneously over expressed and the biological situations in which those genes are over expressed. We explored the relevance of querying...

Author(s): Mathilde Pellerin, and Olivier Gandrillon

  • Article Number: 18B2B3740212

September 2011

Using the ant colony optimization algorithm in the network inference and parameter estimation of biochemical systems

Developing models that can represent biochemical systems is one of the hallmarks of systems biology. Scientists have been gathering data from actual experiments, but there is a lack in computer models that can be used by scientists in analysing the various biochemical systems more effectively. In this research, we propose to use an ant colony optimization (ACO) algorithm for the network inference and parameter...

Author(s): Philip Christian C. Zuniga

  • Article Number: 9BA2E578999

September 2011

Functional equivalence between plant PRORP1 and bacterial RNase P Ribonucleic acid (RNA) raises questions on control and recognition mechanisms

In this short communication we consider the recent results of the successful substitution of theEscherichia coli RNase P ribonucleic acid (RNA) with the Arabidopsis protein enzyme PRORP1. The interest of this result lies in the fact that a plant protein-only enzyme is able to rescue lethal knock-down of the RNA component of bacterial RNase P. Such findings raise interesting questions as well as...

Author(s): Gennaro Auletta, Ivan Colagè, Geoffrey Cook, Paolo D’Ambrosio, Miguel Ramón and Andrew Pinsent

  • Article Number: 4D423029010

July 2011

Pattern clustering of forest fires based on meteorological variables and its classification using hybrid data mining methods

This paper outlines two hybrid approaches to investigate the nonlinear relationship between size of a forest fire and meteorological variables (temperature, relative humidity, wind speed and rainfall). Self organizing map was used to cluster the historical meteorological variables. The clustered data were then used as inputs for two different approaches, the back-propagation neural network and the rule generation...

Author(s): Yong Poh Yu, Rosli Omar, Rhett D. Harrison, Mohan Kumar Sammathuria and Abdul Rahim Nik

  • Article Number: 7F5FF809000

July 2011

Distribution of insertion sequences in Tn1546 element in vancomycin-resistant Staphylococcus aureus in Sulaimani, Kurdistan of Iraq

  In 2008, nine clinical isolates of vancomycin-resistant Staphylococcus aureus containing Tn1546 were recovered in Sulaimani, Iraq. The genetic diversity in Tn1546-like elements has been documented previously. The differences described thus far have included the integration of insertion sequence (IS) elements IS1216V and IS1251. With polymerase chain...

Author(s): Dlnya A. Mohammed and Dana Sabir Khder

  • Article Number: 15F65C68995

March 2011

An intelligent system with the model-view-controller pattern querying visual objects: Application in the malaria control domain

Malaria affects hundreds of millions of people in the world, particularly in the tropics. This results in particularly high death rates among children and pregnant women, especially the poor living in squalid conditions. This situation is not only due to the increasing drug resistance of malaria and the resistance of the main vector to pesticide control, but also the lack of awareness on the part of communities to fight...

Author(s): Guillaume Koum, Augustin Yekel, Bernabé Batchakui and Josiane Etang

  • Article Number: 253B23D8900

March 2011

ATID: Analytical tool for inherited diseases

The body of information surrounding molecular and genomic experiments and clinical investigations is rapidly growing. Bioinformatics tools are software programs that are designed for extracting the meaningful information from the mass of molecular biology/biological databases and carry out sequence or structural analysis. Analytical tool for inherited disease (ATID) is a classification database that can hold the...

Author(s): Hina Iqbal, Iffat Farzana Anjum and Asif Mir

  • Article Number: 34AA04C8911

February 2011

Model-based parameter estimation applied on electrocardiogram signal

An Electrocardiogram (ECG) feature extraction system was developed based on the calculation of the poles employing Pade’s approximation techniques. Pade’s approximation was applied on five different classes of ECG signals’ arrhythmia. Each signal was represented as a rational function of two polynomials of unknown coefficients. Poles were calculated for this rational function for each ECG...

Author(s): A. Moustafa Bani-Hasan , M. Fatma El-Hefnawi and M. Yasser Kadah

  • Article Number: 6F065F340198

February 2011

Prediction of eukaryotic protein subcellular multi-localisation with a combined KNN-SVM ensemble classifier

Proteins may exist in or shift among two or more different subcellular locations, and this phenomenon is closely related to biological function. It is challenging to deal with multiple locations during eukaryotic protein subcellular localisation prediction with routine methods; therefore, a reliable and automatic ensemble classifier for protein subcellular localisation is needed. We propose a new ensemble classifier...

Author(s): Liqi Li, Hong Kuang, Yuan Zhang, Yue Zhou, Kaifa Wang and Ying Wan

  • Article Number: F4CE45D40198

January 2011

Theoretical analysis indicating that human genome is not a blueprint and that human oocytes have the instructions

Is human genome really a blueprint? If it is not a blueprint, how are human bodies constructed? This paper solves this hypothetical proposition. Firstly, it indicates 8 examples of important biological pathways and factors among house-keeping genes and proved that human genome is not a blueprint, but a storage of genes. Secondly, it proved that human oocytes have the instructions for development and differentiation. In...

Author(s): Koichi Itoh

  • Article Number: 399D27C8816

January 2011

An insight into blood clotting disorders in humans

The structure of thrombin protein Oncorhynchus mykiss had not yet been resolved by NMR or X-ray diffraction method. In the present work, we have modeled the structure of protein using Modeller 9v1, taking human thrombin protein as the template. Furthermore, the antithrombin protein was docked with the best model generated by R-dock and Z-dock module of INSIGHT II and the nine potential amino acids involved in...

Author(s): Parul Johri, Sagar Nagare, Kakumani Venkateswara Swamy and Chitta Suresh Kumar

  • Article Number: 6A0AB848835

October 2010

Study of active site and SAR of some benzodiazepines

In the present work, efforts have been made to study the structure activity relationship as well as effect of modelling properties on psychotropic activity of benzodiazepines. The study made by using graph theoretical indices and physicochemical properties. The best model for mathematical calculation of biological activity under consideration is derived in multivariate form using multiple linear regression method and...

Author(s): Mamta Thakur, Lokendra Ojha, Abhilash Thakur and Bal Krishn Solanki

  • Article Number: 30902D38659

October 2010

SNP model to address cytosine trios

DNA methylation maintains allele specific gene expression (Chan et al., 2003) in which miRNA influences allele-specific protein expression and SNPs, found inside miRNA, in turn influences tumor susceptibility (Nicoloso et al., 2010). Further, methylated CpGs have been correlated to APC gene in colorectal cancer (Zhang et al., 2007) and retrotranspositions have also been correlated to APC gene (Miki et al., 1992)....

Author(s): Sriram Kannan

  • Article Number: 72C26AB8667

March 2010

ClustPK: A windows-based cluster analysis tool

There is a great need to develop analytical methodologies to analyze and exploit the information contained in gene expression data obtained from microarray-based experiments. Because of large number of genes and complexity of biological networks, clustering is a useful exploratory technique for analysis of such data. Different data analysis techniques and algorithms have been developed which are used to cluster the gene...

Author(s): Masood ur Rehman Kayani, Umair Shahzad Alam, Farida Anjum and Asif Mir

  • Article Number: C3BA24A8509

March 2010

In silico studies of multi drug resistance (MDR) genetic markers of Plasmodium species

Multi-drug resistance malaria species has been and still is the cause of much morbidity and mortality of malaria throughout the tropics. This epidemic has devastated large populations likewise posed a serious barrier to economic growth in developing countries. The major obstacles however, is it prevention and treatment due to emerging multi-drug resistant (MDR) species. Therefore, anti-malarial drug development needs to...

Author(s): Clarence Suh Yah and Segun Fatumo

  • Article Number: 7AEEE7E8540

November 2009

Chloride anation reaction of aqua (diethylenetriamine) platinum (II): Density functional studies

The nucleophilic and solvolytic path for the chloride anation reaction of aqua(diethylenetriamine)platinum (II) is computationally investigated at the Hartee-Fock (HF) and Density functional theory (B3LYP and mPW1PW91) of levels of calculation in gas phase and on the self- consistent reaction field (SCRF) model. All the stationary points are fully optimized and characterized.  The kinetic and thermodynamic...

Author(s): Partha Sarathi Sengupta, Snehasis Banerjee and Ashish  Kumar Ghosh

  • Article Number: 5C5BCDD8468

November 2009

Prediction of 3D structure of P2RY5 gene and its mutants via comparative homology modelling

3-D Structure of proteins gives valuable insights into the molecular organization, function, docking simulations and also effective drug designing experiments. Autosomal recessive hypotrichosis is a genetic hair disorder that is though not life threatening but it can lead to abhorrent effect on person’s psyche. In the lack of an experimentally determined structure, comparative or homology modeling can provide...

Author(s): Samina Bilal, Hina Iqbal, Farida Anjum and Asif Mir

  • Article Number: F61F5318483

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