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    64 results match your criteria Advances and Applications in Bioinformatics and Chemistry [Journal]

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    Structural and functional characterization of the Helicobacter pylori cytidine 5'-monophosphate-pseudaminic acid synthase PseF: molecular insight into substrate recognition and catalysis mechanism.
    Adv Appl Bioinform Chem 2017 6;10:79-88. Epub 2017 Oct 6.
    Department of Microbiology, University of Chittagong, Chittagong, Bangladesh.
    The bacterium Helicobacter pylori is a human gastric pathogen that can cause a wide range of diseases, including chronic gastritis, peptic ulcer and gastric carcinoma. It is classified as a definitive (class I) human carcinogen by the International Agency for Research on Cancer. Flagella-mediated motility is essential for H. Read More

    Computational tool for optimizing the essential oils utilization in inhibiting the bacterial growth.
    Adv Appl Bioinform Chem 2017 5;10:65-78. Epub 2017 Sep 5.
    Mathematics & Computer Science Dept. Faculty of Science, PortSaid University, PortSaid, Egypt.
    Day after day, the importance of relying on nature in many fields such as food, medical, pharmaceutical industries, and others is increasing. Essential oils (EOs) are considered as one of the most significant natural products for use as antimicrobials, antioxidants, antitumorals, and anti-inflammatories. Optimizing the usage of EOs is a big challenge faced by the scientific researchers because of the complexity of chemical composition of every EO, in addition to the difficulties to determine the best in inhibiting the bacterial activity. Read More

    Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis.
    Adv Appl Bioinform Chem 2017 12;10:57-64. Epub 2017 Jun 12.
    Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy.
    Next-generation sequencing technology has provided resources to easily explore and identify candidate single-nucleotide polymorphisms (SNPs) and variants. However, there remains a challenge in identifying and inferring the causal SNPs from sequence data. A problem with different methods that predict the effect of mutations is that they produce false positives. Read More

    The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling.
    Adv Appl Bioinform Chem 2017 10;10:47-56. Epub 2017 Apr 10.
    Department of Biology and Mathematics, School of Arts, Sciences, and Education, D'Youville College, Buffalo, NY, USA.
    Currently, time-consuming serial in vitro experimentation involving immunocytochemistry or radiolabeled materials is required to identify which of the numerous Rab-GTPases (Rab) and Rab-GTPase activating proteins (RabGAP) are capable of functional interactions. These interactions are essential for numerous cellular functions, and in silico methods of reducing in vitro trial and error would accelerate the pace of research in cell biology. We have utilized a combination of three-dimensional protein modeling and protein bioinformatics to identify domains present in Rab proteins that are predictive of their functional interaction with a specific RabGAP. Read More

    Genetic interrelations in the actinomycin biosynthetic gene clusters of Streptomyces antibioticus IMRU 3720 and Streptomyces chrysomallus ATCC11523, producers of actinomycin X and actinomycin C.
    Adv Appl Bioinform Chem 2017 7;10:29-46. Epub 2017 Apr 7.
    Institut für Chemie, Technische Universität Berlin, Berlin-Charlottenburg.
    Sequencing the actinomycin (acm) biosynthetic gene cluster of Streptomyces antibioticus IMRU 3720, which produces actinomycin X (Acm X), revealed 20 genes organized into a highly similar framework as in the bi-armed acm C biosynthetic gene cluster of Streptomyces chrysomallus but without an attached additional extra arm of orthologues as in the latter. Curiously, the extra arm of the S. chrysomallus gene cluster turned out to perfectly match the single arm of the S. Read More

    In silico-based vaccine design against Ebola virus glycoprotein.
    Adv Appl Bioinform Chem 2017 21;10:11-28. Epub 2017 Mar 21.
    Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh.
    Ebola virus (EBOV) is one of the lethal viruses, causing more than 24 epidemic outbreaks to date. Despite having available molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet for the management and avoidance of EBOV infections in humans. Disclosing this, the present study described an epitope-based peptide vaccine against EBOV, using a combination of B-cell and T-cell epitope predictions, followed by molecular docking and molecular dynamics simulation approach. Read More

    Mapping circulating serum miRNAs to their immune-related target mRNAs.
    Adv Appl Bioinform Chem 2017 2;10:1-9. Epub 2017 Feb 2.
    Systems Immunology Lab; Lab of Integrated Biological Information, Institute for Virus Research Kyoto University, Kyoto, Japan.
    Purpose: Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than non-serum miRNAs.

    Materials And Methods: We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA-mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). Read More

    Molecular docking as a popular tool in drug design, an in silico travel.
    Adv Appl Bioinform Chem 2016 28;9:1-11. Epub 2016 Jun 28.
    University Lille, CNRS UMR8576 UGSF, Lille, France.
    New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism-or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Read More

    Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach.
    Adv Appl Bioinform Chem 2015 8;8:49-63. Epub 2015 Dec 8.
    Biochemistry and Molecular Biology Department, Jahangirnagar University, Savar, Bangladesh ; Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
    Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen's survival but absent in its human host. Read More

    Parallel computing in genomic research: advances and applications.
    Adv Appl Bioinform Chem 2015 13;8:23-35. Epub 2015 Nov 13.
    Institute of Computing, Fluminense Federal University, Niterói, Brazil.
    Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. Read More

    Molecular dynamics simulations: advances and applications.
    Adv Appl Bioinform Chem 2015 19;8:37-47. Epub 2015 Nov 19.
    Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.
    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Read More

    Tools for visualization and analysis of molecular networks, pathways, and -omics data.
    Adv Appl Bioinform Chem 2015 4;8:11-22. Epub 2015 Jun 4.
    Max Planck Institute of Biochemistry, Research Group Computational Biology, Martinsried, Germany.
    Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological network, which denotes a more holistic view on the entanglement of cellular reactions. Biological pathways and networks are not only an appropriate approach to visualize molecular reactions. Read More

    Identification of highly conserved regions in L-segment of Crimean-Congo hemorrhagic fever virus and immunoinformatic prediction about potential novel vaccine.
    Adv Appl Bioinform Chem 2015 8;8:1-10. Epub 2015 Jan 8.
    Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
    Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonotic viral disease with a disease fatality rate between 15% and 70%. Despite the wide range of distribution, the virus (CCHFV) is basically endemic in Africa, Asia, eastern Europe, and the Middle East. Acute febrile illness associated with petechiae, disseminated intravascular coagulation, and multiple-organ failure are the main symptoms of the disease. Read More

    Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis.
    Adv Appl Bioinform Chem 2014 25;7:45-54. Epub 2014 Nov 25.
    Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh.
    Purpose: Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim-sulfamethoxazole, and erythromycin, was observed. Read More

    The hemagglutinin of the influenza A(H1N1)pdm09 is mutating towards stability.
    Adv Appl Bioinform Chem 2014 3;7:37-44. Epub 2014 Oct 3.
    Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico.
    The last influenza A pandemic provided an excellent opportunity to study the adaptation of the influenza A(H1N1)pdm09 virus to the human host. Particularly, due to the availability of sequences taken from isolates since the beginning of the pandemic until date, we could monitor amino acid changes that occurred in the hemagglutinin (HA) as the virus spread worldwide and became the dominant H1N1 strain. HA is crucial to viral infection because it binds to sialidated cell-receptors and mediates fusion of cell and viral membranes; because antibodies that bind to HA may block virus entry to the cell, this protein is subjected to high selective pressure. Read More

    In silico predictive model to determine vector-mediated transport properties for the blood-brain barrier choline transporter.
    Adv Appl Bioinform Chem 2014 2;7:23-36. Epub 2014 Sep 2.
    Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany.
    The blood-brain barrier choline transporter (BBB-ChT) may have utility as a drug delivery vector to the central nervous system (CNS). We therefore initiated molecular docking studies with the AutoDock and AutoDock Vina (ADVina) algorithms to develop predictive models for compound screening and to identify structural features important for binding to this transporter. The binding energy predictions were highly correlated with r(2) =0. Read More

    Three-dimensional quantitative structure-activity relationship and docking studies in a series of anthocyanin derivatives as cytochrome P450 3A4 inhibitors.
    Adv Appl Bioinform Chem 2014 25;7:11-21. Epub 2014 Mar 25.
    Department of Anesthesia and Critical Care, University of Würzburg, Würzburg, Germany.
    The cytochrome P450 (CYP)3A4 enzyme affects the metabolism of most drug-like substances, and its inhibition may influence drug safety. Modulation of CYP3A4 by flavonoids, such as anthocyanins, has been shown to inhibit the mutagenic activity of mammalian cells. Considering the previous investigations addressing CYP3A4 inhibition by these substances, we studied the three-dimensional quantitative structure-activity relationship (3D-QSAR) in a series of anthocyanin derivatives as CYP3A4 inhibitors. Read More

    In silico structure-based screening of versatile P-glycoprotein inhibitors using polynomial empirical scoring functions.
    Adv Appl Bioinform Chem 2014 24;7:1-9. Epub 2014 Mar 24.
    Department of Anesthesia and Critical Care, University of Würzburg, Würzburg, Germany.
    P-glycoprotein (P-gp) is an ATP (adenosine triphosphate)-binding cassette transporter that causes multidrug resistance of various chemotherapeutic substances by active efflux from mammalian cells. P-gp plays a pivotal role in limiting drug absorption and distribution in different organs, including the intestines and brain. Thus, the prediction of P-gp-drug interactions is of vital importance in assessing drug pharmacokinetic and pharmacodynamic properties. Read More

    Hypergeometric analysis of tiling-array and sequence data: detection and interpretation of peaks.
    Adv Appl Bioinform Chem 2013 25;6:55-62. Epub 2013 Oct 25.
    Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands ; Delft Bioinformatics Lab (DBL), Delft University of Technology, Delft, The Netherlands.
    Probing protein-deoxyribonucleic acid (DNA) is gaining popularity as it sheds light on molecular mechanisms that regulate the expression of genes. Currently, tiling-arrays and next-generation sequencing technology can be used to measure these interactions. Both methods generate a signal over the genome in which contiguous regions of peaks on the genome represent the presence of an interacting molecule. Read More

    Design of multiligand inhibitors for the swine flu H1N1 neuraminidase binding site.
    Adv Appl Bioinform Chem 2013 19;6:47-53. Epub 2013 Aug 19.
    Centre for Chemistry and Biotechnology, Deakin University, Geelong, VIC, Australia ; Bigtec Pvt Ltd, Rajajinagar, Bangalore, India.
    Viral neuraminidase inhibitors such as oseltamivir and zanamivir prevent early virus multiplication by blocking sialic acid cleavage on host cells. These drugs are effective for the treatment of a variety of influenza subtypes, including swine flu (H1N1). The binding site for these drugs is well established and they were designed based on computational docking studies. Read More

    Antigenic heterogeneity of capsid protein VP1 in foot-and-mouth disease virus (FMDV) serotype Asia 1.
    Adv Appl Bioinform Chem 2013 13;6:37-46. Epub 2013 Aug 13.
    Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
    Foot and mouth disease virus (FMDV), with its seven serotypes, is a highly contagious virus infecting mainly cloven-hoofed animals. The serotype Asia1 occurs mainly in Asian regions. An in-silico approach was taken to reveal the antigenic heterogeneities within the capsid protein VP1 of Asia1. Read More

    Approaches to the detection of recessive effects using next generation sequencing data from outbred populations.
    Adv Appl Bioinform Chem 2013 11;6:29-35. Epub 2013 Jun 11.
    Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK.
    Conventional methods to analyze genome-wide association studies and whole exome or whole genome sequencing studies would be prone to overlook variants which might exert a recessive effect on risk of disease, either as homozygotes or compound heterozygotes. It is plausible that such effects may be common even in outbred populations. An approach is described which is based on identifying a set of variants in a gene as being potentially of interest and then testing whether there is an excess of cases who are either homozygotes or complex heterozygotes for these variants. Read More

    Inferences on the biochemical and environmental regulation of universal stress proteins from Schistosomiasis parasites.
    Adv Appl Bioinform Chem 2013 10;6:15-27. Epub 2013 May 10.
    Center for Bioinformatics and Computational Biology, Department of Biology, Jackson State University, Jackson, MS, USA ; Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa.
    Background: Human schistosomiasis is a freshwater snail-transmitted disease caused by parasitic flatworms of the Schistosoma genus. Schistosoma haematobium, Schistosoma mansoni, and Schistosoma japonicum are the three major species infecting humans. These parasites undergo a complex developmental life cycle, in which they encounter a plethora of environmental signals. Read More

    Genetic and chemical knockdown: a complementary strategy for evaluating an anti-infective target.
    Adv Appl Bioinform Chem 2013 7;6:1-13. Epub 2013 Feb 7.
    AstraZeneca India R&D, Bangalore, India;
    The equity of a drug target is principally evaluated by its genetic vulnerability with tools ranging from antisense- and microRNA-driven knockdowns to induced expression of the target protein. In order to upgrade the process of antibacterial target identification and discern its most effective type of inhibition, an in silico toolbox that evaluates its genetic and chemical vulnerability leading either to stasis or cidal outcome was constructed and validated. By precise simulation and careful experimentation using enolpyruvyl shikimate-3-phosphate synthase and its specific inhibitor glyphosate, it was shown that genetic knockdown is distinct from chemical knockdown. Read More

    Contact-based ligand-clustering approach for the identification of active compounds in virtual screening.
    Adv Appl Bioinform Chem 2012 6;5:61-79. Epub 2012 Sep 6.
    Université Paris Descartes, Sorbonne, Paris, France.
    Evaluation of docking results is one of the most important problems for virtual screening and in silico drug design. Modern approaches for the identification of active compounds in a large data set of docked molecules use energy scoring functions. One of the general and most significant limitations of these methods relates to inaccurate binding energy estimation, which results in false scoring of docked compounds. Read More

    A novel biclustering approach with iterative optimization to analyze gene expression data.
    Adv Appl Bioinform Chem 2012 7;5:23-59. Epub 2012 Sep 7.
    Department of Biological Sciences, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan ; Graduate School of Information Sciences, Tohoku University, Miyagi, Japan.
    Objective: With the dramatic increase in microarray data, biclustering has become a promising tool for gene expression analysis. Biclustering has been proven to be superior over clustering in identifying multifunctional genes and searching for co-expressed genes under a few specific conditions; that is, a subgroup of all conditions. Biclustering based on a genetic algorithm (GA) has shown better performance than greedy algorithms, but the overlap state for biclusters must be treated more systematically. Read More

    B-Pred, a structure based B-cell epitopes prediction server.
    Adv Appl Bioinform Chem 2012 25;5:11-21. Epub 2012 Jul 25.
    Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
    The ability to predict immunogenic regions in selected proteins by in-silico methods has broad implications, such as allowing a quick selection of potential reagents to be used as diagnostics, vaccines, immunotherapeutics, or research tools in several branches of biological and biotechnological research. However, the prediction of antibody target sites in proteins using computational methodologies has proven to be a highly challenging task, which is likely due to the somewhat elusive nature of B-cell epitopes. This paper proposes a web-based platform for scoring potential immunological reagents based on the structures or 3D models of the proteins of interest. Read More

    A rapid method for combined analysis of common and rare variants at the level of a region, gene, or pathway.
    Adv Appl Bioinform Chem 2012 24;5:1-9. Epub 2012 Jul 24.
    Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK.
    Previously described methods for the combined analysis of common and rare variants have disadvantages such as requiring an arbitrary classification of variants or permutation testing to assess statistical significance. Here we propose a novel method which implements a weighting scheme based on allele frequencies observed in both cases and controls. Because the test is unbiased, scores can be analyzed with a standard t-test. Read More

    Role of Shwachman-Bodian-Diamond syndrome protein in translation machinery and cell chemotaxis: a comparative genomics approach.
    Adv Appl Bioinform Chem 2011 21;4:43-50. Epub 2011 Sep 21.
    Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom; Fellowship for the Interpretation of Genomes, Burr Ridge, IL, USA.
    Shwachman-Bodian-Diamond syndrome (SBDS) is linked to a mutation in a single gene. The SBDS proinvolved in RNA metabolism and ribosome-associated functions, but SBDS mutation is primarily linked to a defect in polymorphonuclear leukocytes unable to orient correctly in a spatial gradient of chemoattractants. Results of data mining and comparative genomic approaches undertaken in this study suggest that SBDS protein is also linked to tRNA metabolism and translation initiation. Read More

    FDR-FET: an optimizing gene set enrichment analysis method.
    Adv Appl Bioinform Chem 2011 15;4:37-42. Epub 2011 Mar 15.
    Applied Genomics, Research and Development, Bristol-Myers Squibb, Pennington, NJ, USA.
    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as "gene sets". Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. Read More

    Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study.
    Adv Appl Bioinform Chem 2011 8;4:29-36. Epub 2011 Mar 8.
    Department of Biotechnology, Bharathiar University, Coimbator, TN, India.
    Background: The human progesterone receptor (hPR) belongs to the steroid receptor family. It may be found as monomers (A and B) and or as a dimer (AB). hPR is regarded as the prognostic biomarker for breast cancer. Read More

    LifePrint: a novel k-tuple distance method for construction of phylogenetic trees.
    Adv Appl Bioinform Chem 2011 20;4:13-27. Epub 2011 Jan 20.
    Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, Mexico City, Mexico.
    Purpose: Here we describe LifePrint, a sequence alignment-independent k-tuple distance method to estimate relatedness between complete genomes.

    Methods: We designed a representative sample of all possible DNA tuples of length 9 (9-tuples). The final sample comprises 1878 tuples (called the LifePrint set of 9-tuples; LPS9) that are distinct from each other by at least two internal and noncontiguous nucleotide differences. Read More

    MODENA: a multi-objective RNA inverse folding.
    Adv Appl Bioinform Chem 2011 22;4:1-12. Epub 2010 Dec 22.
    Graduate School of Science and Technology, Hirosaki University, Hirosaki, Japan.
    Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure. Read More

    SNP analysis of follistatin gene associated with polycystic ovarian syndrome.
    Adv Appl Bioinform Chem 2010 13;3:111-9. Epub 2010 Dec 13.
    Department of Zoology, Presidency College, Chennai, Tamil Nadu, India.
    Follistatin has been reported as a candidate gene for polycystic ovarian syndrome (PCOS) based on linkage and association studies. In this study, investigation of polymorphisms in the FST gene was done to determine if genetic variation is associated with susceptibility to PCOS. The nucleotide sequence of human follistatin and the protein sequence of human follistatin were retrieved from the NCBI database using Entrez. Read More

    A kinetic platform for in silico modeling of the metabolic dynamics in Escherichia coli.
    Adv Appl Bioinform Chem 2010 7;3:97-110. Epub 2010 Dec 7.
    Cellworks Research India Pvt. Ltd, Bangalore, India.
    Background: A prerequisite for a successful design and discovery of an antibacterial drug is the identification of essential targets as well as potent inhibitors that adversely affect the survival of bacteria. In order to understand how intracellular perturbations occur due to inhibition of essential metabolic pathways, we have built, through the use of ordinary differential equations, a mathematical model of 8 major Escherichia coli pathways.

    Results: Individual in vitro enzyme kinetic parameters published in the literature were used to build the network of pathways in such a way that the flux distribution matched that reported from whole cells. Read More

    Construction of random perfect phylogeny matrix.
    Adv Appl Bioinform Chem 2010 16;3:89-96. Epub 2010 Nov 16.
    National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
    Purpose: Interest in developing methods appropriate for mapping increasing amounts of genome-wide molecular data are increasing rapidly. There is also an increasing need for methods that are able to efficiently simulate such data.

    Patients And Methods: In this article, we provide a graph-theory approach to find the necessary and sufficient conditions for the existence of a phylogeny matrix with k nonidentical haplotypes, n single nucleotide polymorphisms (SNPs), and a population size of m for which the minimum allele frequency of each SNP is between two specific numbers a and b. Read More

    Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits.
    Adv Appl Bioinform Chem 2010 28;3:75-88. Epub 2010 Oct 28.
    Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden.
    We present a two-phase strategy for optimizing a multidimensional, nonconvex function arising during genetic mapping of quantitative traits. Such traits are believed to be affected by multiple so called quantitative trait loci (QTL), and searching for d QTL results in a d-dimensional optimization problem with a large number of local optima. We combine the global algorithm DIRECT with a number of local optimization methods that accelerate the final convergence, and adapt the algorithms to problem-specific features. Read More

    An unsupervised strategy for biomedical image segmentation.
    Adv Appl Bioinform Chem 2010 13;3:67-73. Epub 2010 Sep 13.
    Digital Signal Processing Group, Institute of Cybernetics, Mathematics, and Physics, Havana, Cuba.
    Many segmentation techniques have been published, and some of them have been widely used in different application problems. Most of these segmentation techniques have been motivated by specific application purposes. Unsupervised methods, which do not assume any prior scene knowledge can be learned to help the segmentation process, and are obviously more challenging than the supervised ones. Read More

    Modeling of thermodynamic and physico-chemical properties of coumarins bioactivity against Candida albicans using a Levenberg-Marquardt neural network.
    Adv Appl Bioinform Chem 2010 13;3:59-66. Epub 2010 Aug 13.
    Department of Biotechnology, School of Pharmacy, Zanjan University of Medical Science, Zanjan, Iran.
    In recent years, due to vital need for novel fungicidal agents, investigation on natural antifungal resources has been increased. The special features exhibited by neural network classifiers make them suitable for handling complex problems like analyzing different properties of candidate compounds in computer-aided drug design. In this study, by using a Levenberg-Marquardt (LM) neural network (the fastest of the training algorithms), the relation between some important thermodynamic and physico-chemical properties of coumarin compounds and their biological activities (tested against Candida albicans) has been evaluated. Read More

    Molecular biocoding of insulin.
    Adv Appl Bioinform Chem 2010 28;3:45-58. Epub 2010 Jul 28.
    Novi Travnik, Kalinska, Bosnia and Herzegovina.
    This paper discusses cyberinformation studies of the amino acid composition of insulin, in particular the identification of scientific terminology that could describe this phenomenon, ie, the study of genetic information, as well as the relationship between the genetic language of proteins and theoretical aspects of this system and cybernetics. The results of this research show that there is a matrix code for insulin. It also shows that the coding system within the amino acid language gives detailed information, not only on the amino acid "record", but also on its structure, configuration, and various shapes. Read More

    Pharmacogenomics of drug efficacy in the interferon treatment of chronic hepatitis C using classification algorithms.
    Adv Appl Bioinform Chem 2010 15;3:39-44. Epub 2010 Jun 15.
    Department of Internal Medicine, Kuang Tien General Hospital, Taichung County, Taiwan.
    Chronic hepatitis C (CHC) patients often stop pursuing interferon-alfa and ribavirin (IFN-alfa/RBV) treatment because of the high cost and associated adverse effects. It is highly desirable, both clinically and economically, to establish tools to distinguish responders from nonresponders and to predict possible outcomes of the IFN-alfa/RBV treatments. Single nucleotide polymorphisms (SNPs) can be used to understand the relationship between genetic inheritance and IFN-alfa/RBV therapeutic response. Read More

    Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization.
    Adv Appl Bioinform Chem 2010 9;3:25-38. Epub 2010 Jun 9.
    Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, Paris, France.
    We explore, using the Crh protein dimer as a model, how information from solution NMR, solid-state NMR and X-ray crystallography can be combined using structural bioinformatics methods, in order to get insights into the transition from solution to crystal. Using solid-state NMR chemical shifts, we filtered intra-monomer NMR distance restraints in order to keep only the restraints valid in the solid state. These filtered restraints were added to solid-state NMR restraints recorded on the dimer state to sample the conformational landscape explored during the oligomerization process. Read More

    Insights into the classification of small GTPases.
    Adv Appl Bioinform Chem 2010 21;3:15-24. Epub 2010 May 21.
    Department of Bioinformatics, Center for Medical Biotechnology, University of Duisburg- Essen, Essen, Germany.
    In this study we used a Random Forest-based approach for an assignment of small guanosine triphosphate proteins (GTPases) to specific subgroups. Small GTPases represent an important functional group of proteins that serve as molecular switches in a wide range of fundamental cellular processes, including intracellular transport, movement and signaling events. These proteins have further gained a special emphasis in cancer research, because within the last decades a huge variety of small GTPases from different subgroups could be related to the development of all types of tumors. Read More

    Predicting recurrent aphthous ulceration using genetic algorithms-optimized neural networks.
    Adv Appl Bioinform Chem 2010 14;3:7-13. Epub 2010 May 14.
    Faculty of Dentistry, University of Jordan, Amman, Jordan.
    Objective: To construct and optimize a neural network that is capable of predicting the occurrence of recurrent aphthous ulceration (RAU) based on a set of appropriate input data.

    Participants And Methods: Artificial neural networks (ANN) software employing genetic algorithms to optimize the architecture neural networks was used. Input and output data of 86 participants (predisposing factors and status of the participants with regards to recurrent aphthous ulceration) were used to construct and train the neural networks. Read More

    Estimating affinities of calcium ions to proteins.
    Adv Appl Bioinform Chem 2010 15;3:1-6. Epub 2010 Mar 15.
    Department of Bioinformatics/Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.
    Ca(2+)-ions have a range of affinities to different proteins, depending on the various functions of these proteins. This makes the determination of Ca(2+)-protein affinities an interesting subject for functional studies. We have investigated the performance of two methods - Fold-X and AutoDock vina - in the prediction of Ca(2+)-protein affinities. Read More

    Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies.
    Adv Appl Bioinform Chem 2009 3;2:125-38. Epub 2009 Dec 3.
    Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany.
    Genotoxic stress is induced by a broad range of DNA-damaging agents and could lead to a variety of human diseases including cancer. DNA damage is also therapeutically induced for cancer treatment with the aim to eliminate tumor cells. However, the effectiveness of radio- and chemotherapy is strongly hampered by tumor cell resistance. Read More

    Computer applications for prediction of protein-protein interactions and rational drug design.
    Adv Appl Bioinform Chem 2009 10;2:101-23. Epub 2009 Nov 10.
    Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
    In recent years, protein-protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current efforts into the structural proteomics programs. Given that experimental determination of many protein-protein complex structures is highly challenging, and in the context of current high-performance computational capabilities, different computer tools are being developed to help in this task. Read More

    Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.
    Adv Appl Bioinform Chem 2009 22;2:79-100. Epub 2009 Sep 22.
    Institute of Medical Science, University of Tokyo, Tokyo, Japan.
    Protein-protein docking simulations can provide the predicted complex structural models. In a docking simulation, several putative structural models are selected by scoring functions from an ensemble of many complex models. Scoring functions based on statistical analyses of heterodimers are usually designed to select the complex model with the most abundant interaction mode found among the known complexes, as the correct model. Read More

    Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.
    Adv Appl Bioinform Chem 2009 5;2:71-8. Epub 2009 Jun 5.
    Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, IA, USA.
    The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. Read More

    Performance of PLS regression coefficients in selecting variables for each response of a multivariate PLS for omics-type data.
    Adv Appl Bioinform Chem 2009 13;2:57-70. Epub 2009 May 13.
    Digilab BioVision GmbH, Hannover, Germany.
    Multivariate partial least square (PLS) regression allows the modeling of complex biological events, by considering different factors at the same time. It is unaffected by data collinearity, representing a valuable method for modeling high-dimensional biological data (as derived from genomics, proteomics and peptidomics). In presence of multiple responses, it is of particular interest how to appropriately "dissect" the model, to reveal the importance of single attributes with regard to individual responses (for example, variable selection). Read More

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