Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Seyed Morteza Najibi, Mehdi Maadooliat, Lan Zhou, Jianhua Z. Huang, Xin GaoAbstractRecently, 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 ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Fourier Analysis of Conservation Patterns in Protein Secondary Structure
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Ashok Palaniappan, Eric JakobssonAbstractResidue 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 d...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms
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. The conformation space of the system coor...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Seanna Hewitt, Benjamin Kilian, Ramyya Hari, Tyson Koepke, Richard Sharpe, Amit DhingraAbstractIdentification 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 fo...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Flexible Analog Search with Kernel PCA Embedded Molecule Vectors
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Stefano Rensi, Russ B. AltmanAbstractStudying 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 inclu...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Exploring Components of the CO2-Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome-Based Analysis
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Amornpan Klanchui, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin MeechaiAbstractIn 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 l...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

A random forest classifier for detecting rare variants in NGS data from viral populations
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Raunaq Malhotra, Manjari Jha, Mary Poss, Raj AcharyaAbstractWe 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Hervé Seligmann, Ganesh WarthiAbstractA 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 i...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Pía Francesca Loren Reyes, Tom Michoel, Anagha Joshi, Guillaume DevaillyAbstractFunctional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liver from ove...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Are Circulating Type 2 Vaccine-derived Polioviruses (VDPVs) Genetically Distinguishable from Immunodeficiency-associated VDPVs?
We presented quantitative approaches using genetic information as a surveillance tool for early detection of VDPV outbreaks. This work suggests that genetic variations between cVDPV2 and iVDPV2 may reflect differences in viral micro-environments, host-virus interactions, and selective pressures during person-to-person transmission compared with chronic infections in immunodeficient patients. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Mary Qu Yang, Dan Li, William Yang, Yifan Zhang, Jun Liu, Weida TongAbstractClear cell renal cell carcinoma (ccRCC) is the most common and most aggressive form of renal cell cancer (RCC). The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Ruibang Luo, Fritz J. Sedlazeck, Charlotte A. Darby, Stephen M. Kelly, Michael C. SchatzAbstractLinked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve de novo assembly, haplotype phasing, and other applications. Based on our analysis of 14 datasets, we introduce LRSim that simulates linked-reads by emulating the library preparation and sequencing process with fine control over variants, linked-read characteristics, and the short-read profile. We conclud...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Functional Roles for Exosomal MicroRNAs in the Tumour Microenvironment
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Emma Bell, Molly A. TaylorAbstractExtracellular microRNAs are released from cells both passively and actively. The presence of these microRNAs in the tumour microenvironment (TME) can significantly impact on the plasticity of cancer cells leading to the promotion of metastatic and angiogenic processes. These extracellular microRNAs can act not only on other cancer cells, but also cells present in the TME, such as immune cells, endothelial cells, fibroblasts, and others acting to subvert the host immune system and drive tum...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Worsening of Verbal Fluency After Deep Brain Stimulation in Parkinson's Disease: A Focused Review
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Andreas Højlund, Mikkel V. Petersen, Kousik Sarathy Sridharan, Karen ØstergaardAbstractWorsening of verbal fluency after treatment with deep brain stimulation in Parkinson's disease patients is one of the most often reported cognitive adverse effect. The underlying mechanisms of this decline are not well understood. The present focused review assesses the evidence for the reliability of the often-reported decline of verbal fluency, as well as the evidence for the suggested mechanisms including disease progres...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Chagas disease research and development: Is there light at the end of the tunnel?
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Eric ChatelainAbstractChagas disease, or American trypanosomiasis, is the result of infection by the parasite Trypanosoma cruzi. It is endemic in Latin America, and spreading around the globe due to human migration. Although it was first identified more than a century ago, only two old drugs are available for treatment and a lot of questions related to the disease progression, its pathologies, and not to mention the assessment of treatment efficacy, are subject to debate and remain to be answered. Indeed, the current statu...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Flexible Gastro-intestinal Endoscopy — Clinical Challenges and Technical Achievements
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Niehls Kurniawan, Martin KeuchelAbstractFlexible 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 autofluor...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

What can mathematical modelling say about CHO metabolism and protein glycosylation?
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Sarah N. Galleguillos, David Ruckerbauer, Matthias P. Gerstl, Nicole Borth, Michael Hanscho, Jürgen ZanghelliniAbstractChinese 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 mos...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Antibody H3 Structure Prediction
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): C. Marks, C.M. DeaneAbstractAntibodies 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. T...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Multi-level and hybrid modelling approaches for systems biology
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): R. Bardini, G. Politano, A. Benso, S. Di CarloAbstractDuring 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Dynamic Programming Based Segmentation in Biomedical Imaging
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Kathrin Ungru, Xiaoyi JiangAbstractMany 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 t...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Re-imagining the future of diagnosis of Neglected Tropical Diseases
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Rosanna W. Peeling, Debrah I. Boeras, John NkengasongAbstractNeglected 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Combinations of Genetic Variants Occurring Exclusively in Patients
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Erling Mellerup, Gert Lykke MøllerAbstractIn 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 poly...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Time-resolved biophysical approaches to nucleocytoplasmic transport
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Francesco CardarelliAbstractMolecules 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 develo...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Protein post-translational modifications: In silico prediction tools and molecular modeling
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Martina Audagnotto, Matteo Dal PeraroAbstractPost-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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Toshihiko Sugiki, Naohiro Kobayashi, Toshimichi FujiwaraAbstractNuclear 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 r...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Resurrecting the Dead (Molecules)
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Jan Zaucha, Jonathan G. HeddleAbstractBiological 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Regulation of Metabolic Pathways by MarR Family Transcription Factors
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Anne GroveAbstractBacteria have evolved sophisticated mechanisms for regulation of metabolic pathways. Such regulatory circuits ensure that anabolic pathways remain repressed unless final products are in short supply and that catabolic enzymes are not produced in absence of their substrates. The precisely tuned gene activity underlying such circuits is in the purview of transcription factors that may bind pathway intermediates, which in turn modulate transcription factor function and therefore gene expression. This review ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree
We present the R software package SigTree, a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Scalability and Validation of Big Data Bioinformatics Software
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Andrian Yang, Michael Troup, Joshua W.K. HoAbstractThis 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Zekun Yin, Haidong Lan, Guangming Tan, Mian Lu, Athanasios V. Vasilakos, Weiguo LiuAbstractThe 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Corrigendum to “Searching for drug synergy in complex dose–response landscapes using an interaction potency model” [Comput. Struct. Biotechnol. J. 13 (2015) 504–513]
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Jing Tang (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Pranav Kulkarni, Peter FrommoltAbstractWhile Next-Generation Sequencing (NGS) can now be considered an established analysis technology for research applications across the life sciences, the analysis workflows still require substantial bioinformatics expertise. Typical challenges include the appropriate selection of analytical software tools, the speedup of the overall procedure using HPC parallelization and acceleration technology, the development of automation strategies, data storage solutions and finally the developmen...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Are the Symptoms of Parkinsonism Cortical in Origin?
We present three reasons to suspect that the major deleterious consequence of dopamine loss from the striatum is a cortical malfunction. We suggest that it is cortex, rather than striatum, that should be considered as the source of the debilitating symptoms of Parkinson's disease (PD) since:1.Cortical synapses onto striatal dendritic spines are lost in PD.2.All known treatments of the symptoms of PD disrupt beta oscillations. Oscillations that are also disrupted following antidromic activation of cortical neurons.3.The final output of basal ganglia directly modulates thalamic connections to layer I of frontal cortical area...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Heart Failure: Diagnosis, Severity Estimation and Prediction of Adverse Events Through Machine Learning Techniques
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Evanthia E. Tripoliti, Theofilos G. Papadopoulos, Georgia S. Karanasiou, Katerina K. Naka, Dimitrios I. FotiadisAbstractHeart failure is a serious condition with high prevalence (about 2% in the adult population in developed countries, and more than 8% in patients older than 75 years). About 3–5% of hospital admissions are linked with heart failure incidents. Heart failure is the first cause of admission by healthcare professionals in their clinical practice. The costs are very high, reaching up to 2% of the tot...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Karel Sedlar, Kristyna Kupkova, Ivo ProvaznikAbstractOne of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenom...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Mining textural knowledge in biological images: Applications, methods and trends
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Santa Di Cataldo, Elisa FicarraAbstractTexture analysis is a major task in many areas of computer vision and pattern recognition, including biological imaging. Indeed, visual textures can be exploited to distinguish specific tissues or cells in a biological sample, to highlight chemical reactions between molecules, as well as to detect subcellular patterns that can be evidence of certain pathologies. This makes automated texture analysis fundamental in many applications of biomedicine, such as the accurate detection and gr...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Matched Molecular Pair Analysis in Short: Algorithms, Applications and Limitations
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Christian Tyrchan, Emma EvertssonAbstractMolecular matched pair (MMP) analysis has been used for more than 40 years within molecular design and is still an important tool to analyse potency data and other compound properties. The methods used to find matched pairs range from manual inspection, through supervised methods to unsupervised methods, which are able to find previously unknown molecular pairs. Recent publications demonstrate the value of automatic MMP analysis of publicly available bioactivity databases. The ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Machine Learning and Data Mining Methods in Diabetes Research
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Ioannis Kavakiotis, Olga Tsave, Athanasios Salifoglou, Nicos Maglaveras, Ioannis Vlahavas, Ioanna ChouvardaAbstractThe remarkable advances in biotechnology and health sciences have led to a significant production of data, such as high throughput genetic data and clinical information, generated from large Electronic Health Records (EHRs). To this end, application of machine learning and data mining methods in biosciences is presently, more than ever before, vital and indispensable in efforts to transform intelligently all a...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering
We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Biobetters From an Integrated Computational/Experimental Approach
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Serdar Kuyucak, Veysel KayserAbstractBiobetters are new drugs designed from existing peptide or protein-based therapeutics by improving their properties such as affinity and selectivity for the target epitope, and stability against degradation. Computational methods can play a key role in such design problems—by predicting the changes that are most likely to succeed, they can drastically reduce the number of experiments to be performed. Here we discuss the computational and experimental methods commonly used in drug ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Tuhin Kumar Guha, Alvan Wai, Georg HausnerAbstractTargeted 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. Th...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Mini-review: In vitro Metabolic Engineering for Biomanufacturing of High-value Products
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Weihua Guo, Jiayuan Sheng, Xueyang FengAbstractWith 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...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Increasing European Support for Neglected Infectious Disease Research
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Ole F. Olesen, Marit AckermannAbstractNeglected 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 pu...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Apolipoprotein E - A Multifunctional Protein with Implications in Various Pathologies as a Result of Its Structural Features
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Irina Florina Tudorache, Violeta Georgeta Trusca, Anca Violeta GafencuAbstractApolipoprotein 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 neurodeg...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Personalized Therapy Against Preeclampsia by Replenishing Placental Protein 13 (PP13) Targeted to Patients With Impaired PP13 Molecule or Function
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Hamutal Meiri, George Osol, Irene Cetin, Sveinbjörn Gizurarson, Berthold HuppertzAbstractHypertensive 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. Biomarker...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase
Publication date: 2017Source: Computational and Structural Biotechnology Journal, Volume 15Author(s): Katja Venko, A. Roy Choudhury, Marjana NovičAbstractThe 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 ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

ctDNA and CTCs in Liquid Biopsy – Current Status and Where We Need to Progress
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Martin H.D. Neumann, Sebastian Bender, Thomas Krahn, Thomas SchlangeAbstractWe discuss the current status of liquid biopsy and its advantages and challenges with a focus on pre-analytical sample handling, technologies and workflows. The potential of circulating tumor cells and circulating tumor DNA is pointed out and an overview of corresponding technologies is given. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones
This report provides the first molecular foundation for the model that the CFBP linker acts as an unstructured, flexible loop, allowing the two flanking chaperone modules function independently while linked in cis, likely to assist in the folding of multisubunit client complexes.Graphical Abstract (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China
In conclusion, a significant change in the gut microbial community was observed in the omnivorous cattle, suggesting that diet may be one of the factors that may signal an adaptation response by the cattle to maintain feed efficiency as a consequence of the change in environment. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Amplification and bioinformatics analysis of conserved FAD-binding region of L-amino acid oxidase (LAAO) genes in gastropods compared to other organisms
This study aimed to investigate the conserved FAD-binding region of the L-amino acid oxidase (LAAO) genes in twelve gastropod genera commonly found in Thailand compared to those in other organisms using molecular cloning, nucleotide sequencing and bioinformatics analysis. Genomic DNA of gastropods and other invertebrates was extracted and screened using primers specific to the conserved FAD-binding region of LAAO. The amplified 143-bp fragments were cloned and sequenced. The obtained nucleotide sequences of 21 samples were aligned and phylogenetically compared to the LAAO-conserved FAD-binding regions of 210 other organism...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research