abstract：Purpose:Mutation-induced variation of protein-ligand binding affinity is the key to many genetic diseases and the emergence of drug resistance, and therefore predicting such mutation impacts is of great importance. In this work, we aim to predict the mutation impacts on protein-ligand binding affinity using efficient s...

journal_title：Computational and structural biotechnology journal

authors： Wang DD,Ou-Yang L,Xie H,Zhu M,Yan H

更新日期：2020-02-20 00:00:00

abstract：:The emergence of recent SARS-CoV-2 has become a global health issue. This single-stranded positive-sense RNA virus is continuously spreading with increasing morbidities and mortalities. The proteome of this virus contains four structural and sixteen nonstructural proteins that ensure the replication of the virus in th...

journal_title：Computational and structural biotechnology journal

authors： Khan A,Tahir Khan M,Saleem S,Junaid M,Ali A,Shujait Ali S,Khan M,Wei DQ

更新日期：2020-01-01 00:00:00

abstract：:Coronaviruses are a group of enveloped RNA viruses that are diversely found in humans and now declared a global pandemic by the World Health Organization in March 2020. The population's susceptibility to these highly pathogenic coronaviruses has contributed to large outbreaks, evolved into public health events, and ra...

journal_title：Computational and structural biotechnology journal

authors： Singh DD,Han I,Choi EH,Yadav DK

更新日期：2020-01-01 00:00:00

abstract：:SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor - angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-ca...

journal_title：Computational and structural biotechnology journal

authors： Chowdhury R,Boorla VS,Maranas CD

更新日期：2020-01-01 00:00:00

abstract：:The impacts of environmental chemicals on the decline of kidney function have been suggested by a limited number of statistical and animal studies. Thus, those exposures may be modifiable risk factors for chronic kidney disease. Some of the chemicals, such as Perfluoroalkyl acid (PFA), are pervasive throughout our env...

journal_title：Computational and structural biotechnology journal

authors： Zhao J,Hinton P,Chen J,Jiang J

更新日期：2019-12-17 00:00:00

abstract：:The long noncoding RNAs (lncRNAs) are ubiquitous in organisms and play crucial role in a variety of biological processes and complex diseases. Emerging evidences suggest that lncRNAs interact with corresponding proteins to perform their regulatory functions. Therefore, identifying interacting lncRNA-protein pairs is t...

journal_title：Computational and structural biotechnology journal

authors： Yi HC,You ZH,Cheng L,Zhou X,Jiang TH,Li X,Wang YB

更新日期：2019-11-30 00:00:00

abstract：:Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding...

journal_title：Computational and structural biotechnology journal

authors： Yang W,Sun X,Zhang C,Lai L

更新日期：2019-11-11 00:00:00

abstract：:Natural products (NPs) are an indispensable source of drugs and they have a better coverage of the pharmacological space than synthetic compounds, owing to their high structural diversity. The prediction of their interaction profiles with druggable protein targets remains a major challenge in modern drug discovery. Ex...

journal_title：Computational and structural biotechnology journal

authors： Moumbock AFA,Li J,Mishra P,Gao M,Günther S

更新日期：2019-10-28 00:00:00

abstract：:Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown ...

journal_title：Computational and structural biotechnology journal

authors： Bai F,Cai Z,Yang L

更新日期：2019-10-25 00:00:00

abstract：:RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and cha...

journal_title：Computational and structural biotechnology journal

authors： Zhao J,Li Q,Li Y,He X,Zheng Q,Huang S

更新日期：2019-08-07 00:00:00

abstract：:Bacteria sense temporal changes in extracellular stimuli via sensory signal transducers and move by rotating flagella towards into a favorable environment for their survival. Each flagellum is a supramolecular motility machine consisting of a bi-directional rotary motor, a universal joint and a helical propeller. The ...

journal_title：Computational and structural biotechnology journal

authors： Minamino T,Kinoshita M,Namba K

更新日期：2019-07-31 00:00:00

abstract：:Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the mod...

journal_title：Computational and structural biotechnology journal

authors： Escalante DE,Aksan A

更新日期：2019-06-11 00:00:00

abstract：:Lutein, a hydroxylated carotenoid, is a pigment synthesised by plants and bacteria. Animals are unable to synthesise lutein, nevertheless, it is present in animal tissues, where its only source is dietary intake. Both in plants and animals, carotenoids are associated mainly with membranes where they carry out importan...

journal_title：Computational and structural biotechnology journal

authors： Makuch K,Markiewicz M,Pasenkiewicz-Gierula M

更新日期：2019-04-06 00:00:00

abstract：:In this review we aim to summarize studies investigating the impact of a molecular profiling (MP)-guided treatment approach in heavily pretreated cancer patients. In summary, many independent single- and multicenter studies showed a significant benefit of MP-guided treatment regarding response rates and survival. Howe...

journal_title：Computational and structural biotechnology journal

authors： Zimmer K,Kocher F,Spizzo G,Salem M,Gastl G,Seeber A

更新日期：2019-03-26 00:00:00

abstract：:Lung cancer is the leading worldwide cause of cancer mortality, however, neither curative treatments nor substantial prolonged survival has been achieved, highlighting the need for investigating new proteins responsible for its development and progression. IKKα is an essential protein for cell survival and differentia...

journal_title：Computational and structural biotechnology journal

authors： Page A,Ortega A,Alameda JP,Navarro M,Paramio JM,Saiz-Pardo M,Almeida EI,Hernández P,Fernández-Aceñero MJ,García-Fernández RA,Casanova ML

更新日期：2019-02-07 00:00:00

abstract：:As knowledge of the genetics behind inflammatory bowel disease (IBD) has continually improved, there has been a demand for methods that can use this data in a clinically significant way. Genome-wide association analyses for IBD have identified 232 risk genetic loci for the disorder. While identification of these risk ...

journal_title：Computational and structural biotechnology journal

authors： Grenier L,Hu P

更新日期：2019-01-07 00:00:00

abstract：Purpose:The goal of this study is to set an empirical baseline to map the structure-function relation of the antigens from the commercialized vaccine products. Methods:To study the structural changes of protein antigens after adsorption several analytical tools including DLS, FTIR, Fluorescence, LD, and SEM have been ...

journal_title：Computational and structural biotechnology journal

authors： Kalbfleisch K,Deshmukh S,Mei C,Ore M,Williams W,Durowoju I,Duprez J,Morin S,Carpick B,Kirkitadze M

更新日期：2018-11-29 00:00:00

abstract：:Traditional Chinese Medicine (TCM) has a long history of widespread clinical applications, especially in East Asia, and is becoming frequently used in Western countries. However, owing to extreme complicacy in both chemical ingredients and mechanism of action, a deep understanding of TCM is still difficult. To acceler...

journal_title：Computational and structural biotechnology journal

authors： Li B,Ma C,Zhao X,Hu Z,Du T,Xu X,Wang Z,Lin J

更新日期：2018-11-23 00:00:00

abstract：:An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characteriz...

journal_title：Computational and structural biotechnology journal

authors： Csizmadia G,Farkas B,Spagina Z,Tordai H,Hegedűs T

更新日期：2018-10-18 00:00:00

abstract：:Biomedical research and clinical decision depend increasingly on scientific evidence realized by a number of authoritative databases, mostly public and continually enriched via peer scientific contributions. Given the dynamic nature of biomedical evidence data and their usage in the sensitive domain of biomedical scie...

journal_title：Computational and structural biotechnology journal

authors： Kleinaki AS,Mytis-Gkometh P,Drosatos G,Efraimidis PS,Kaldoudi E

更新日期：2018-08-17 00:00:00

abstract：:Industrial bioreactors range from 10.000 to 700.000 L and characteristically show different zones of substrate availabilities, dissolved gas concentrations and pH values reflecting physical, technical and economic constraints of scale-up. Microbial producers are fluctuating inside the bioreactors thereby experiencing ...

journal_title：Computational and structural biotechnology journal

authors： Zieringer J,Takors R

更新日期：2018-07-06 00:00:00

abstract：:Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evol...

journal_title：Computational and structural biotechnology journal

authors： Tsang CC,Tang JYM,Lau SKP,Woo PCY

更新日期：2018-05-31 00:00:00

abstract：:The field of machine learning has allowed researchers to generate and analyse vast amounts of data using a wide variety of methodologies. Artificial Neural Networks (ANN) are some of the most commonly used statistical models and have been successful in biomarker discovery studies in multiple disease types. This review...

journal_title：Computational and structural biotechnology journal

authors： Zafeiris D,Rutella S,Ball GR

更新日期：2018-02-21 00:00:00

abstract：:Functional 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 functiona...

journal_title：Computational and structural biotechnology journal

authors： Reyes PFL,Michoel T,Joshi A,Devailly G

更新日期：2017-08-26 00:00:00

abstract：: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 s...

journal_title：Computational and structural biotechnology journal

authors： Olesen OF,Ackermann M

更新日期：2017-01-19 00:00:00

abstract：:Immunotherapy is the revolution in cancer treatment of this last decade. Among multiple approaches able to harness the power of the immune system against cancer, T cell based immunotherapies represent one of the most successful examples. In particular, biotechnological engineering of protein structures, like the T cel...

journal_title：Computational and structural biotechnology journal

authors： Ruella M,Maus MV

更新日期：2016-09-28 00:00:00

abstract：:Target based chemical screens are a mainstay of modern drug discovery, but the effectiveness of this reductionist approach is being questioned in light of declines in pharmaceutical R & D efficiency. In recent years, phenotypic screens have gained increasing acceptance as a complementary/alternative approach to early ...

journal_title：Computational and structural biotechnology journal

authors： Williams CH,Hong CC

更新日期：2016-09-18 00:00:00

abstract：:Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure-function understanding of this superfamily is still developin...

journal_title：Computational and structural biotechnology journal

authors： Li D,Moorman R,Vanhercke T,Petrie J,Singh S,Jackson CJ

更新日期：2016-09-12 00:00:00

abstract：:The field of dentistry lacks satisfactory tools to help visualize planned procedures and their potential results to patients. Dentists struggle to provide an effective image in their patient's mind of the end results of the planned treatment only through verbal explanations. Thus, verbal explanations alone often canno...

journal_title：Computational and structural biotechnology journal

authors： Canbazoglu E,Salman YB,Yildirim ME,Merdenyan B,Ince IF

更新日期：2016-06-29 00:00:00

abstract：:Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and ...

journal_title：Computational and structural biotechnology journal

authors： Dona AC,Kyriakides M,Scott F,Shephard EA,Varshavi D,Veselkov K,Everett JR

更新日期：2016-03-09 00:00:00

abstract：:Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players...

journal_title：Computational and structural biotechnology journal

authors： Chandrasekaran S,Bonchev D

更新日期：2016-02-10 00:00:00

abstract：:With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related ...

journal_title：Computational and structural biotechnology journal

authors： Fronza R,Vasciaveo A,Benso A,Schmidt M

更新日期：2015-11-30 00:00:00

abstract：:Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively...

journal_title：Computational and structural biotechnology journal

authors： Petri V,Hayman GT,Tutaj M,Smith JR,Laulederkind S,Wang SJ,Nigam R,De Pons J,Shimoyama M,Dwinell MR

更新日期：2015-11-26 00:00:00

abstract：:The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS) has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic...

journal_title：Computational and structural biotechnology journal

authors： Swaminathan R,Huang Y,Moosavinasab S,Buckley R,Bartlett CW,Lin SM

更新日期：2015-10-31 00:00:00

abstract：:One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs) change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structure...

journal_title：Computational and structural biotechnology journal

authors： Wang D,Song L,Singh V,Rao S,An L,Madhavan S

更新日期：2015-09-30 00:00:00

abstract：:Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout th...

journal_title：Computational and structural biotechnology journal

authors： Das K,Chowdhury P,Ganguly S

更新日期：2015-09-04 00:00:00

abstract：:Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evol...

journal_title：Computational and structural biotechnology journal

authors： Foley J

更新日期：2015-07-26 00:00:00

abstract：:BOG (Bacterium and virus analysis of Orthologous Groups) is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Clusters of Orthologous Groups (COGs) that are enriched among genes that have gone through sig...

journal_title：Computational and structural biotechnology journal

authors： Park J,Taslim C,Lin S

更新日期：2015-05-21 00:00:00

abstract：:New variants of β-1,4-galactanase from the mesophilic organism Aspergillus aculeatus were designed using the structure of β-1,4-galactanase from the thermophile organism Myceliophthora thermophila as a template. Some of the variants were generated using PROPKA 3.0, a validated pKa prediction tool, to test its usefulne...

journal_title：Computational and structural biotechnology journal

authors： Torpenholt S,De Maria L,Olsson MH,Christensen LH,Skjøt M,Westh P,Jensen JH,Lo Leggio L

更新日期：2015-04-09 00:00:00

abstract：:A fundamental question in biology is how complex structures are maintained after their initial specification. We address this question by reviewing the role of the Hox gene Abd-B in Drosophila testis organogenesis, which proceeds through embryonic, larval and pupal stages to reach maturation in adult stages. The data ...

journal_title：Computational and structural biotechnology journal

authors： Papagiannouli F,Lohmann I

更新日期：2015-01-21 00:00:00