Computational Enzyme Design: Advances, hurdles and possible ways forward.

abstract：:Recent years have witnessed a spurt of activities in the elucidation of the molecular function of a class of proteins with great potential in biomass degradation. GH61 proteins are of fungal origin and were originally classified in family 61 of the glycoside hydrolases. From the beginning they were strongly suspected ...

journal_title：Computational and structural biotechnology journal

authors： Lo Leggio L,Welner D,De Maria L

更新日期：2012-11-30 00:00:00

abstract：:Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU) mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC) physiology and structural integrity that may impact on blood component storage ...

journal_title：Computational and structural biotechnology journal

authors： Kildey K,Flower RL,Tran TV,Tunningley R,Harris J,Dean MM

更新日期：2013-09-23 00:00:00

abstract：:Biased agonism, the ability of agonists to differentially activate downstream signaling pathways by stabilizing specific receptor conformations, is a key issue for G protein-coupled receptor (GPCR) signaling. The C-terminal domain might influence this functional selectivity of GPCRs as it engages G proteins, GPCR kina...

journal_title：Computational and structural biotechnology journal

authors： Navarro G,Gonzalez A,Campanacci S,Rivas-Santisteban R,Reyes-Resina I,Casajuana-Martin N,Cordomí A,Pardo L,Franco R

更新日期：2020-09-24 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：: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：: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：: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：:Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact tha...

journal_title：Computational and structural biotechnology journal

authors： Grădinaru C,Lopacińska JM,Huth J,Kestler HA,Flyvbjerg H,Mølhave K

更新日期：2012-11-21 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：: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 human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transpor...

journal_title：Computational and structural biotechnology journal

authors： Tangella LP,Arooj M,Deplazes E,Gray ES,Mancera RL

更新日期：2020-12-30 00:00:00

abstract：:Although the potential advantages of clinical germline genome editing (GGE) over currently available methods are limited, the implementation of GGE in the clinic has been proposed and discussed. Ethical issues related to such an application have been extensively debated, meanwhile, seemingly less attention has been pa...

journal_title：Computational and structural biotechnology journal

authors： Niemiec E,Howard HC

更新日期：2020-03-21 00:00:00

abstract：:Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with ...

journal_title：Computational and structural biotechnology journal

authors： Meijering E

更新日期：2020-08-07 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：: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：: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：: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：: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：:Biomimetic design of new materials uses nature as antetype, learning from billions of years of evolution. This work emphasizes the mechanical and tribological properties of skin, combining both hardness and wear resistance of its surface (the stratum corneum) with high elasticity of the bulk (epidermis, dermis, hypode...

journal_title：Computational and structural biotechnology journal

authors： Lackner JM,Waldhauser W,Major L,Teichert C,Hartmann P

更新日期：2013-05-08 00:00:00

abstract：:The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulat...

journal_title：Computational and structural biotechnology journal

authors： Jiao J,Tian CF

更新日期：2020-11-19 00:00:00

abstract：Purpose:Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral fat. Methods:We recruited 32 obese adults and 30 healthy controls at baseline. Among the obese subjects, 14 subjects underwent laparoscopic sl...

journal_title：Computational and structural biotechnology journal

authors： Nie X,Chen J,Ma X,Ni Y,Shen Y,Yu H,Panagiotou G,Bao Y

更新日期：2020-09-20 00:00:00

abstract：:Metabolomics is a relatively new high-throughput technology that aims at measuring all endogenous metabolites within a biological sample in an unbiased fashion. The resulting metabolic profiles may be regarded as functional signatures of the physiological state, and have been shown to comprise effects of genetic regul...

journal_title：Computational and structural biotechnology journal

authors： Bartel J,Krumsiek J,Theis FJ

更新日期：2013-03-22 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：:Recent high-throughput structure-sensitive genome-wide sequencing-based assays have enabled large-scale studies of RNA structure, and robust transcriptome-wide computational prediction of individual RNA structures across RNA classes from these assays has potential to further improve the prediction accuracy. Here, we d...

journal_title：Computational and structural biotechnology journal

authors： Kuksa PP,Li F,Kannan S,Gregory BD,Leung YY,Wang LS

更新日期：2020-06-08 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：: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：:Recent years have witnessed the tendency of measuring a biological sample on multiple omics scales for a comprehensive understanding of how biological activities on varying levels are perturbed by genetic variants, environments, and their interactions. This new trend raises substantial challenges to data integration a...

journal_title：Computational and structural biotechnology journal

authors： Baldwin E,Han J,Luo W,Zhou J,An L,Liu J,Zhang HH,Li H

更新日期：2020-03-05 00:00:00

abstract：:Circular RNA (circRNA) plays an important role in the development of diseases, and it provides a novel idea for drug development. Accurate identification of circRNAs is important for a deeper understanding of their functions. In this study, we developed a new classifier, CirRNAPL, which extracts the features of nuclei...

journal_title：Computational and structural biotechnology journal

authors： Niu M,Zhang J,Li Y,Wang C,Liu Z,Ding H,Zou Q,Ma Q

更新日期：2020-04-02 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：: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