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Computational and Structural Biotechnology Journal

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28280526/protein-structure-classification-and-loop-modeling-using-multiple-ramachandran-distributions
#11
Seyed Morteza Najibi, Mehdi Maadooliat, Lan Zhou, Jianhua Z Huang, Xin Gao
Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28228927/computational-approaches-for-revealing-the-structure-of-membrane-transporters-case-study-on-bilitranslocase
#12
REVIEW
Katja Venko, A Roy Choudhury, Marjana Novič
The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28228926/antibody-h3-structure-prediction
#13
REVIEW
C Marks, C M Deane
Antibodies are proteins of the immune system that are able to bind to a huge variety of different substances, making them attractive candidates for therapeutic applications. Antibody structures have the potential to be useful during drug development, allowing the implementation of rational design procedures. The most challenging part of the antibody structure to experimentally determine or model is the H3 loop, which in addition is often the most important region in an antibody's binding site. This review summarises the approaches used so far in the pursuit of accurate computational H3 structure prediction...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28228925/what-can-mathematical-modelling-say-about-cho-metabolism-and-protein-glycosylation
#14
REVIEW
Sarah N Galleguillos, David Ruckerbauer, Matthias P Gerstl, Nicole Borth, Michael Hanscho, Jürgen Zanghellini
Chinese hamster ovary cells have been in the spotlight for process optimization in recent years, due to being the major, long established cell factory for the production of recombinant proteins. A deep, quantitative understanding of CHO metabolism and mechanisms involved in protein glycosylation has proven to be attainable through the development of high throughput technologies. Here we review the most notable accomplishments in the field of modelling CHO metabolism and protein glycosylation.
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28217262/the-effects-of-shared-information-on-semantic-calculations-in-the-gene%C3%A2-ontology
#15
Paul W Bible, Hong-Wei Sun, Maria I Morasso, Rasiah Loganantharaj, Lai Wei
The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179981/deep-assessment-of-genomic-diversity-in-cassava-for-herbicide-tolerance-and-starch-biosynthesis
#16
Jorge Duitama, Lina Kafuri, Daniel Tello, Ana María Leiva, Bernhard Hofinger, Sneha Datta, Zaida Lentini, Ericson Aranzales, Bradley Till, Hernán Ceballos
Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179980/increasing-european-support-for-neglected-infectious-disease-research
#17
REVIEW
Ole F Olesen, Marit Ackermann
Neglected infectious diseases (NIDs) are a persistent cause of death and disability in low-income countries. Currently available drugs and vaccines are often ineffective, costly or associated with severe side-effects. Although the scale of research on NIDs does not reflect their disease burden, there are encouraging signs that NIDs have begun to attract more political and public attention, which have translated into greater awareness and increased investments in NID research by both public and private donors...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179979/flexible-gastro-intestinal-endoscopy-clinical-challenges-and-technical-achievements
#18
REVIEW
Niehls Kurniawan, Martin Keuchel
Flexible gastro-intestinal (GI) endoscopy is an integral diagnostic and therapeutic tool in clinical gastroenterology. High quality standards for safety, patients' comfort, and efficiency have already been achieved. Clinical challenges and technical approaches are discussed in this short review. Image enhanced endoscopy for further characterization of mucosal and vascular patterns includes dye-spray or virtual chromoendoscopy. For confocal laser endoscopy, endocytoscopy, and autofluorescence clinical value has not yet been finally evaluated...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179978/mini-review-in-vitro-metabolic-engineering-for-biomanufacturing-of-high-value-products
#19
REVIEW
Weihua Guo, Jiayuan Sheng, Xueyang Feng
With the breakthroughs in biomolecular engineering and synthetic biology, many valuable biologically active compound and commodity chemicals have been successfully manufactured using cell-based approaches in the past decade. However, because of the high complexity of cell metabolism, the identification and optimization of rate-limiting metabolic pathways for improving the product yield is often difficult, which represents a significant and unavoidable barrier of traditional in vivo metabolic engineering. Recently, some in vitro engineering approaches were proposed as alternative strategies to solve this problem...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179977/programmable-genome-editing-tools-and-their-regulation-for-efficient-genome-engineering
#20
REVIEW
Tuhin Kumar Guha, Alvan Wai, Georg Hausner
Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break...
2017: Computational and Structural Biotechnology Journal
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