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Computational and Structural Biotechnology Journal

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https://www.readbyqxmd.com/read/29034064/personalized-therapy-against-preeclampsia-by-replenishing-placental-protein-13-pp13-targeted-to-patients-with-impaired-pp13-molecule-or-function
#1
REVIEW
Hamutal Meiri, George Osol, Irene Cetin, Sveinbjörn Gizurarson, Berthold Huppertz
Hypertensive disorders affect about one third of all people aged 20 and above, and are treated with anti-hypertensive drugs. Preeclampsia (PE) is one form of such disorders that only develops during pregnancy. It affects ten million pregnant women globally and additionally causes fetal loss and major newborn disabilities. The syndrome's origin is multifactorial, and anti-hypertensive drugs are ineffective in treating it. Biomarkers are helpful for predict its development. Generic drugs, such as low dose aspirin, were proven effective in preventing preterm PE...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28924459/genetic-code-optimization-for-cotranslational-protein-folding-codon-directional-asymmetry-correlates-with-antiparallel-betasheets-trna-synthetase-classes
#2
Hervé Seligmann, Ganesh Warthi
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28883909/computing-platforms-for-big-biological-data-analytics-perspectives-and-challenges
#3
REVIEW
Zekun Yin, Haidong Lan, Guangming Tan, Mian Lu, Athanasios V Vasilakos, Weiguo Liu
The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28855977/multi-level-and-hybrid-modelling-approaches-for-systems-biology
#4
REVIEW
R Bardini, G Politano, A Benso, S Di Carlo
During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28819548/a-random-forest-classifier-for-detecting-rare-variants-in-ngs-data-from-viral-populations
#5
Raunaq Malhotra, Manjari Jha, Mary Poss, Raj Acharya
We propose a random forest classifier for detecting rare variants from sequencing errors in Next Generation Sequencing (NGS) data from viral populations. The method utilizes counts of varying length of k-mers from the reads of a viral population to train a Random forest classifier, called MultiRes, that classifies k-mers as erroneous or rare variants. Our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. Frames are sets of non-orthogonal basis functions that were traditionally used in signal processing for noise removal...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28794828/scalability-and-validation-of-big-data-bioinformatics-software
#6
REVIEW
Andrian Yang, Michael Troup, Joshua W K Ho
This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28748045/sigtree-a-microbial-community-analysis-tool-to-identify-and-visualize-significantly-responsive-branches-in-a-phylogenetic-tree
#7
REVIEW
John R Stevens, Todd R Jones, Michael Lefevre, Balasubramanian Ganesan, Bart C Weimer
Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28660014/apolipoprotein-e-a-multifunctional-protein-with-implications-in-various-pathologies-as-a-result-of-its-structural-features
#8
REVIEW
Irina Florina Tudorache, Violeta Georgeta Trusca, Anca Violeta Gafencu
Apolipoprotein E (apoE), a 34 kDa glycoprotein, mediates hepatic and extrahepatic uptake of plasma lipoproteins and cholesterol efflux from lipid-laden macrophages. In humans, three structural different apoE isoforms occur, with subsequent functional changes and pathological consequences. Here, we review data supporting the involvement of apoE structural domains and isoforms in normal and altered lipid metabolism, cardiovascular and neurodegenerative diseases, as well as stress-related pathological states...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28652896/resurrecting-the-dead-molecules
#9
REVIEW
Jan Zaucha, Jonathan G Heddle
Biological molecules, like organisms themselves, are subject to genetic drift and may even become "extinct". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of "molecular resurrection" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28652895/exploring-components-of-the-co2-concentrating-mechanism-in-alkaliphilic-cyanobacteria-through-genome-based-analysis
#10
Amornpan Klanchui, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin Meechai
In cyanobacteria, the CO2-concentrating mechanism (CCM) is a vital biological process that provides effective photosynthetic CO2 fixation by elevating the CO2 level near the active site of Rubisco. This process enables the adaptation of cyanobacteria to various habitats, particularly in CO2-limited environments. Although CCM of freshwater and marine cyanobacteria are well studied, there is limited information on the CCM of cyanobacteria living under alkaline environments. Here, we aimed to explore the molecular components of CCM in 12 alkaliphilic cyanobacteria through genome-based analysis...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28487762/modern-technologies-of-solution-nuclear-magnetic-resonance-spectroscopy-for-three-dimensional-structure-determination-of-proteins-open-avenues-for-life-scientists
#11
REVIEW
Toshihiko Sugiki, Naohiro Kobayashi, Toshimichi Fujiwara
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28458783/flexible-analog-search-with-kernel-pca-embedded-molecule-vectors
#12
Stefano Rensi, Russ B Altman
Studying analog series to find structural transformations that enhance the activity and ADME properties of lead compounds is an important part of drug development. Matched molecular pair (MMP) search is a powerful tool for analog analysis that imitates researchers' ability to select pairs of compounds that differ only by small well-defined transformations. Abstraction is a challenge for existing MMP search algorithms, which can result in the omission of relevant, inexact MMPs, and inclusion of irrelevant, contextually dissimilar MMPs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28458782/protein-post-translational-modifications-in-silico-prediction-tools-and-molecular-modeling
#13
REVIEW
Martina Audagnotto, Matteo Dal Peraro
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28435614/time-resolved-biophysical-approaches-to-nucleocytoplasmic-transport
#14
REVIEW
Francesco Cardarelli
Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28392892/evaluation-of-multiple-approaches-to-identify-genome-wide-polymorphisms-in-closely-related-genotypes-of-sweet-cherry-prunus-avium-l
#15
Seanna Hewitt, Benjamin Kilian, Ramyya Hari, Tyson Koepke, Richard Sharpe, Amit Dhingra
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28377798/combinations-of-genetic-variants-occurring-exclusively-in-patients
#16
REVIEW
Erling Mellerup, Gert Lykke Møller
In studies of polygenic disorders, scanning the genetic variants can be used to identify variant combinations. Combinations that are exclusively found in patients can be separated from those combinations occurring in control persons. Statistical analyses can be performed to determine whether the combinations that occur exclusively among patients are significantly associated with the investigated disorder. This research strategy has been applied in materials from various polygenic disorders, identifying clusters of patient-specific genetic variant combinations that are significant associated with the investigated disorders...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28377797/evaluation-of-the-novel-algorithm-of-flexible-ligand-docking-with-moveable-target-protein-atoms
#17
Alexey V Sulimov, Dmitry A Zheltkov, Igor V Oferkin, Danil C Kutov, Ekaterina V Katkova, Eugene E Tyrtyshnikov, Vladimir B Sulimov
We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28352456/re-imagining-the-future-of-diagnosis-of-neglected-tropical-diseases
#18
REVIEW
Rosanna W Peeling, Debrah I Boeras, John Nkengasong
Neglected Tropical Diseases (NTDs) affect an estimated 1 billion people in 149 countries. The World Health Organization (WHO) prioritised 17 NTDs for control and elimination by 2020 and defined a Road Map to help countries reach these goals. Improved diagnostics for NTDs are essential for guiding treatment strategies at different thresholds of control, interruption of transmission, elimination and post-elimination surveillance. While substantial progress has been made in the last decade with chemotherapy, the same cannot be said of diagnostics, largely due to the perceived lack of a commercially viable market for NTD diagnostics...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28316759/fourier-analysis-of-conservation-patterns-in-protein-secondary-structure
#19
Ashok Palaniappan, Eric Jakobsson
Residue conservation is a common observation in alignments of protein families, underscoring positions important in protein structure and function. Though many methods measure the level of conservation of particular residue positions, currently we do not have a way to study spatial oscillations occurring in protein conservation patterns. It is known that hydrophobicity shows spatial oscillations in proteins, which is characterized by computing the hydrophobic moment of the protein domains. Here, we advance the study of moments of conservation of protein families to know whether there might exist spatial asymmetry in the conservation patterns of regular secondary structures...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28289536/dynamic-programming-based-segmentation-in-biomedical-imaging
#20
REVIEW
Kathrin Ungru, Xiaoyi Jiang
Many applications in biomedical imaging have a demand on automatic detection of lines, contours, or boundaries of bones, organs, vessels, and cells. Aim is to support expert decisions in interactive applications or to include it as part of a processing pipeline for automatic image analysis. Biomedical images often suffer from noisy data and fuzzy edges. Therefore, there is a need for robust methods for contour and line detection. Dynamic programming is a popular technique that satisfies these requirements in many ways...
2017: Computational and Structural Biotechnology Journal
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