Abstract：
:Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.
journal_name
Int J Mol Scijournal_title
International journal of molecular sciencesauthors
Moal IH,Bates PAdoi
10.3390/ijms11103623subject
Has Abstractpub_date
2010-09-28 00:00:00pages
3623-48issue
10issn
1422-0067journal_volume
11pub_type
杂志文章abstract：:Genistein has been reported to stimulate luminal HCO3(-) secretion. We hypothesized that genistein mediates this effect via SLC26A6 and SLC4A4 (NBCe1) transporters. Our study aimed to: investigate changes in uterine fluid pH, Na+ and HCO3(-) concentration and expression of uterine SLC26A6 and NBCe1 under genistein eff...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms15010958
更新日期：2014-01-10 00:00:00
abstract：:Free fatty acids (FFAs) are cytotoxic to pancreatic islet β-cells and play a crucial role in the diabetes disease process. A recent study revealed a down-regulation of transcription factor 2 (TCF2) levels during FFA-mediated cytotoxicity in pancreatic β-cells. However, its function during this process and the underlyi...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms150813317
更新日期：2014-07-30 00:00:00
abstract：:Clipping of recombinant proteins is a major issue in animal cell cultures. A recombinant Fc-fusion protein, VEGFR1(D1-D3)-Fc expressed in CHOK1SV GS-KO cells was observed to be undergoing clippings in lab scale cultures. Partial cleaving of expressed protein initiated early on in cell culture and was observed to incre...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms17060913
更新日期：2016-06-09 00:00:00
abstract：:Higher prevalence of neurodegenerative diseases is strictly connected with progressive aging of the world population. Interestingly, a broad range of age-related, neurodegenerative diseases is characterized by a common pathological mechanism-accumulation of misfolded and unfolded proteins within the cells. Under certa...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms21062108
更新日期：2020-03-19 00:00:00
abstract：:One of the ultimate goals of wound healing research is to find effective healing techniques that utilize the regeneration of similar tissues. This involves the modification of various wound dressing biomaterials for proper wound management. The biopolymer chitosan (beta-1,4-D-glucosamine) has natural biocompatibility ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms10031300
更新日期：2009-03-01 00:00:00
abstract：:One of the most common causes of mortality and morbidity in children is perinatal hypoxia-ischemia (HI). In spite of the advances in neonatology, its incidence is not diminishing, generating a pediatric population that will require an extended amount of chronic care throughout their lifetime. For this reason, new and ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms14059379
更新日期：2013-04-29 00:00:00
abstract：:Articular cartilage is a structure lack of vascular distribution. Once the cartilage is injured or diseased, it is unable to regenerate by itself. Surgical treatments do not effectively heal defects in articular cartilage. Tissue engineering is the most potential solution to this problem. In this study, methoxy poly(e...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms19041125
更新日期：2018-04-09 00:00:00
abstract：:Environmental or biomedical exposure to nanoparticles (NPs) can results in translocation and accumulation of NPs in the brain, which can lead to health-related problems. NPs have been shown to induce toxicity to neuronal cells through several direct mechanisms, but only a few studies have also explored the indirect ef...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21197030
更新日期：2020-09-24 00:00:00
abstract：:The objectives of this investigation were to produce a novel chitosanase for application in industries and waste treatment. The transformation of chitinous biowaste into valuable bioactive chitooligomers (COS) is one of the most exciting applications of chitosanase. An amphiprotic novel chitosanase from Bacillus mycoi...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms17081302
更新日期：2016-08-10 00:00:00
abstract：:Addition of hydrogen peroxide (H2O2) is a method commonly used to trigger cellular oxidative stress. However, the doses used (often hundreds of micromolar) are disproportionally high with regard to physiological oxygen concentration (low micromolar). In this study using polarographic measurement of oxygen concentratio...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21239149
更新日期：2020-11-30 00:00:00
abstract：:In the protozoan ciliate Euplotes, a transduction pathway resulting in a mitogenic cell growth response is activated by autocrine receptor binding of cell type-specific, water-borne signaling protein pheromones. In Euplotes raikovi, a marine species of temperate waters, this transduction pathway was previously shown t...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms14047457
更新日期：2013-04-03 00:00:00
abstract：:Estrogen receptor-α positive (ERα⁺) breast cancers represent 75% of all invasive breast cancer cases, while de novo or acquired resistance to ER-directed therapy is also on the rise. Numerous factors contribute to this phenomenon including the recently-reported ESR1 gene mutations such as Y537S, which amplifies co-act...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms19020579
更新日期：2018-02-15 00:00:00
abstract：:Brain-derived neurothrophic factor (BDNF) is a neurotrophin expressed in different tissues and cells, including neurons, endothelial cells, leukocytes, megakaryocytes and platelets. Modifications of BDNF in plasma and/or in serum are associated with neurodegenerative and psychiatric disorders, cardiovascular diseases,...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms18091987
更新日期：2017-09-15 00:00:00
abstract：:Colon cancer is an aggressive tumor form with a poor prognosis. This study reports a comparative proteomic analysis performed by using two-dimensional differential in-gel electrophoresis (2D-DIGE) between 26 pooled colon cancer surgical tissues and adjacent non-tumoral tissues, to identify potential target proteins co...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21093096
更新日期：2020-04-28 00:00:00
abstract：:Alzheimer's disease (AD) is a leading cause of dementia worldwide, associated with cognitive deficits and brain glucose metabolic alteration. However, the associations of glucose metabolic changes with cognitive dysfunction are less detailed. Here, we examined the brains of APP/presenilin 1 (PS1) transgenic (Tg) mice ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms17101707
更新日期：2016-10-18 00:00:00
abstract：:Polygalacturonase (PG), a large hydrolase family in plants, is involved in pectin disassembly of the cell wall in plants. The present study aims to characterize PG genes and investigate their expression patterns in Solanum lycopersicum. We identified 54 PG genes in the tomato genome and compared their amino acid seque...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms19082290
更新日期：2018-08-04 00:00:00
abstract：:In the development of drugs, we sometimes encounter fatty change of the hepatocytes (steatosis) which is not accompanied by degenerative change in the liver in non-clinical toxicity studies. In this study, we investigated the relationships between fatty change of the hepatocytes noted in non-clinical toxicity studies ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms18040810
更新日期：2017-04-12 00:00:00
abstract：:Osteoporosis represents the most common bone disease worldwide and results in a significantly increased fracture risk. Extrinsic and intrinsic factors implicated in the development of osteoporosis are also associated with delayed fracture healing and impaired bone regeneration. Based on a steadily increasing life expe...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms20010083
更新日期：2018-12-26 00:00:00
abstract：:Epidermal keratinocytes represent a rich source of C-C motif chemokine 20 (CCL20) and recruit CCR6+ interleukin (IL)-17A-producing T cells that are known to be pathogenic for psoriasis. A previous study revealed that scratch injury on keratinocytes upregulates CCL20 production, which is implicated in the Koebner pheno...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21020434
更新日期：2020-01-09 00:00:00
abstract：:The demise of retinal ganglion cells (RGCs) is characteristic of diseases of the retina such as glaucoma and diabetic or ischemic retinopathies. Pigment epithelium-derived factor (PEDF) is a multifunctional secreted protein that mediates neuroprotection and inhibition of angiogenesis in the retina. We have studied exp...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms22010369
更新日期：2020-12-31 00:00:00
abstract：:To date, viruses are reported to be responsible for more than 15% of all tumors worldwide. The oncogenesis could be influenced directly by the activity of viral oncoproteins or by the chronic infection or inflammation. The group of human oncoviruses includes Epstein–Barr virus (EBV), human papillomavirus (HPV), ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms19041217
更新日期：2018-04-17 00:00:00
abstract：:Pompe disease is a glycogen storage disease caused by a deficiency in acid α-glucosidase (GAA), a hydrolase necessary for the degradation of lysosomal glycogen. This deficiency in GAA results in muscle and neuronal glycogen accumulation, which causes respiratory insufficiency. Pompe disease mouse models provide a mean...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms21062256
更新日期：2020-03-24 00:00:00
abstract：:Obesity is a risk factor for Alzheimer's disease (AD), but underlying mechanisms are not clear. We analyzed peripheral clearance of amyloid β (Aβ) in overweight mice because its systemic elimination may impact brain Aβ load, a major landmark of AD pathology. We also analyzed whether circulating insulin-like growth fac...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21249675
更新日期：2020-12-18 00:00:00
abstract：:Genistein, daidzein, glycitein and quercetin are flavonoids present in soybean and other vegetables in high amounts. These flavonoids can be metabolically converted to more active forms, which may react with guanine in the DNA to form complexes and can lead to DNA depurination. We assumed two ultimate carcinogen forms...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms13021269
更新日期：2012-01-01 00:00:00
abstract：:Mercaptopyruvate sulfurtransferase (Mpst) and its homolog thiosulfate sulfurtransferase (Tst = rhodanese) detoxify cyanide to thiocyanate. Mpst is attracting attention as one of the four endogenous hydrogen sulfide (H2S)/reactive sulfur species (RSS)-producing enzymes, along with cystathionine β-synthase (Cbs), cystat...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21030818
更新日期：2020-01-27 00:00:00
abstract：:The mushroom Inonotus obliquus has been widely used as a folk medicine in Russia, Poland and most of the Baltic countries. In this study, water-soluble and alkali-soluble crude polysaccharides (IOW and IOA) were isolated from I. obliquus, and the carbohydrate-rich fractions IOW-1 and IOA-1 were obtained respectively a...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms13079194
更新日期：2012-01-01 00:00:00
abstract：:Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms18112442
更新日期：2017-11-17 00:00:00
abstract：:Up to 30-50% of patients with locally advanced prostate cancer (PCa) undergoing radiotherapy (RT) experience biochemical recurrence (BCR). The immune system affects the RT response. Immunogenetics could define new biomarkers for personalization of PCa patients' treatment. The aim of this study is to define the immunog...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms20092082
更新日期：2019-04-27 00:00:00
abstract：:Blunt snout bream (Megalobrama amblycephala) is a widely favored herbivorous fish species and is a frequentlyused fish model for studying the metabolism physiology. This study aimed to provide a comprehensive illustration of the mechanisms of a high-starch diet (HSD) induced lipid metabolic disorder by identifying mic...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms18061161
更新日期：2017-05-31 00:00:00
abstract：:Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms161226129
更新日期：2015-12-03 00:00:00
