Abstract:
:A diffusion theory-based, all-physical ab initio protein folding simulation is described and applied. The model is based upon the drift and diffusion of protein substructures relative to one another in the multiple energy fields present. Without templates or statistical inputs, the simulations were run at physiologic and ambient temperatures (including pH). Around 100 protein secondary structures were surveyed, and twenty tertiary structures were determined. Greater than 70% of the secondary core structures with over 80% alpha helices were correctly identified on protein ranging from 30 to 200 amino-acid sequence. The drift-diffusion model predicted tertiary structures with RMSD values in the 3-5 Angstroms range for proteins ranging 30 to 150 amino acids. These predictions are among the best for an all ab initio protein simulation. Simulations could be run entirely on a desktop computer in minutes; however, more accurate tertiary structures were obtained using molecular dynamic energy relaxation. The drift-diffusion model generated realistic energy versus time traces. Rapid secondary structures followed by a slow compacting towards lower energy tertiary structures occurred after an initial incubation period in agreement with observations.
journal_name
Biomed Res Intjournal_title
BioMed research internationalauthors
Kang Y,Fortmann CMdoi
10.1155/2013/583045subject
Has Abstractpub_date
2013-01-01 00:00:00pages
583045eissn
2314-6133issn
2314-6141journal_volume
2013pub_type
杂志文章abstract:Materials and Methods:Various aqueous extracts were prepared from this plant and preadministered per os to albino mice 3 h before APAP administration, once daily for one week. Animals from the normal group were given only distilled water while those from negative control received only APAP 250 mg/kg. After treatment, m...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/3807234
更新日期:2020-08-31 00:00:00
abstract::Craniofacial development consists of a highly complex sequence of the orchestrated growth and fusion of facial processes. It is also known that craniofacial abnormalities can be detected in 1/3 of all patients with congenital diseases. Within the various craniofacial abnormalities, orofacial clefting is one of the mos...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2015/901041
更新日期:2015-01-01 00:00:00
abstract::Molecular epidemiology has revealed that Mycobacterium tuberculosis (Mtb), formerly regarded as highly conserved species, displays a considerable degree of genetic variability that can influence the outcome of the disease as well as the innate and adaptive immune response. Recent studies have demonstrated that Mtb fam...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/741309
更新日期:2014-01-01 00:00:00
abstract::Coconut palm (Cocos nucifera) is an important commercial crop in many tropical countries, but its industry generates large amounts of residue. One way to address this problem is to use this residue, coconut husk, to produce second-generation (2G) ethanol. The aim of this review is to describe the methods that have bee...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2018/4916497
更新日期:2018-09-27 00:00:00
abstract::Upon allergen challenge, DC subsets are recruited to target sites under the influence of chemotactic agents; however, details pertinent to their trafficking remain largely unknown. We investigated the kinetic profiles of blood and skin-infiltrating DC subsets in twelve atopic subjects receiving six weekly intradermal ...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2014/231036
更新日期:2014-01-01 00:00:00
abstract:OBJECT:Video-assisted thoracoscopic sympathectomy is a safe, effective, and minimally invasive procedure for primary hyperhidrosis. This study aims to evaluate long-term results and patients' quality of life and investigate potential variables responsible for compensatory sweating after one-stage bilateral single-port ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/348017
更新日期:2013-01-01 00:00:00
abstract::In the past decade, much emphasis has been put on the transcriptional activation of HIV-1, which is proposed as a promised strategy for eradicating latent HIV-1 provirus. Two drugs, prostratin and hexamethylene bisacetamide (HMBA), have shown potent effects as inducers for releasing HIV-1 latency when used alone or in...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2016/5173205
更新日期:2016-01-01 00:00:00
abstract::A bioenergetical analysis of swimming at intensities near competitive distances is inexistent. It was aimed to compare the transient VO2 kinetics responses and metabolic contributions whilst swimming at different velocities around VO2max. 12 trained male swimmers performed (i) an incremental protocol to determine the ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/675363
更新日期:2014-01-01 00:00:00
abstract:Background:Yes-associated protein 1 (YAP1) is an effector of Hippo pathway, which plays a significant role in cell proliferation and tumor progression. The relationship between YAP1 and gastrointestinal cancer has been explored in many previous studies. We conducted a meta-analysis to explore the prognostic effect of Y...
journal_title:BioMed research international
pub_type: 杂志文章,meta分析
doi:10.1155/2018/4039173
更新日期:2018-11-14 00:00:00
abstract::One of the biggest obstetric challenges is the diagnosis and management of a short cervix as cervical length has an inverse relationship with risk of preterm birth. A cervical cerclage is a surgical procedure to reduce the risk of preterm birth and can be placed in an elective or emergency setting. This is a retrospec...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章,多中心研究
doi:10.1155/2018/2065232
更新日期:2018-09-30 00:00:00
abstract::To investigate white matter (WM) abnormalities in neocortical epilepsy, we extract supratentorial WM parameters from raw tensor magnetic resonance images (MRI) with automated region-of-interest (ROI) registrations. Sixteen patients having neocortical seizures with secondarily generalised convulsions and 16 age-matched...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/419376
更新日期:2014-01-01 00:00:00
abstract:Objective:The objective was to study the risk and protective factors involved in retinal vascular development of preterm infants with retinopathy of prematurity. Methods:Between 2000 and 2017, 185 preterm infants were included in the protocol for retinopathy of prematurity. Risk factors associated with speed of retina...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/2721578
更新日期:2019-04-24 00:00:00
abstract::Keratinases are proteolytic enzymes predominantly active when keratin substrates are available that attack disulfide bridges in the keratin to convert them from complex to simplified forms. Keratinases are essential in preparation of animal nutrients, protein supplements, leather manufacture, textile processing, deter...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2015/140726
更新日期:2015-01-01 00:00:00
abstract::The Toll-Like receptor 4 (TLR4) plays an important role in immunity, tissue repair, and regeneration. The objective of the present work was to evaluate the association of TLR4 single nucleotide polymorphisms (SNPs) rs4986790, rs4986791, rs11536858 (merged into rs10759931), rs1927911, and rs1927914 with increased diabe...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/318686
更新日期:2013-01-01 00:00:00
abstract:Introduction:This study examines the utility of electroencephalography (EEG) in clinical decision making in acute ischemic stroke (AIS) patients in regards to the prescription of antiseizure medications. Methods:Patients were grouped as having positive EEG (+) for epileptiform activity or negative EEG (-). These studi...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/6250531
更新日期:2020-12-19 00:00:00
abstract::In spite of the declining incidence of gastric cancer (GC) in recent years, the mortality rate is still high. The asymptomatic nature and nonspecific clinical manifestations combined with the lack of efficient screening programs delay the diagnosis of GC. Therefore, the prevalence of advanced gastric cancer (AGC) has ...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2016/3923585
更新日期:2016-01-01 00:00:00
abstract:OBJECTIVES:Most developmental processes are under the control of small regulatory RNAs called microRNAs (miRNAs). We hypothesize that different fetal developmental processes might be reflected by extracellular miRNAs in maternal plasma and may be utilized as biomarkers for the noninvasive prenatal diagnosis of chromoso...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/402475
更新日期:2014-01-01 00:00:00
abstract::A standard protocol of dosimetric measurements is used by the organizations responsible for verifying that the doses delivered in radiation-therapy institutions are within authorized limits. This study evaluated a self-designed simple auditing phantom for use in verifying the dose of radiation therapy; the phantom des...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/934387
更新日期:2015-01-01 00:00:00
abstract::This study documented the population dynamics of Biomphalaria and associated natural infections with digenetic trematodes, along the shores of Lake Albert and Lake Victoria, recording local physicochemical factors. Over a two-and-a-half-year study period with monthly sampling, physicochemical factors were measured at ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/717261
更新日期:2015-01-01 00:00:00
abstract::This research investigated the protective role of Leea macrophylla extract on CCl4-induced acute liver injury in rats. Different fractions of Leea macrophylla (Roxb.) crude extract were subjected to analysis for antioxidative effects. Rats were randomly divided into four groups as normal control, hepatic control, and ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/356729
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Tumor patients and patients after traumas are endangered by a reduced immune defense, and a silver coating on their megaprostheses may reduce their risks of infection. The aim of this study was to determine the silver ion concentration directly measured from the periprosthetic tissue and the influence on the...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/763096
更新日期:2013-01-01 00:00:00
abstract::Ezrin, coding protein EZR which cross-links actin filaments, overexpresses and involves invasion, metastasis, and poor prognosis in various cancers including esophageal squamous cell carcinoma (ESCC). In our previous study, Ezrin was knock down and analyzed by mRNA expression profile which has not been fully mined. In...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/651954
更新日期:2014-01-01 00:00:00
abstract:Aim:To evaluate thiol/disulphide homeostasis as a new indicator of oxidative stress in AKI patients and to determine the effect of HD on antioxidant balance and oxidative stress through plasma thiols. Methods:This study was performed in patients aged between 12 months and 18 years prospectively who underwent hemodialy...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2018/1898671
更新日期:2018-09-25 00:00:00
abstract::Contrast-induced acute kidney injury (CI-AKI) is commonly defined as a decline in kidney function occurring in a narrow time window after administration of iodinated contrast material. The incidence of AKI after contrast material administration greatly depends on the specific definition and cutoff values used. Althoug...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2014/859328
更新日期:2014-01-01 00:00:00
abstract:OBJECTIVE:Fever in systemic lupus erythematosus (SLE) can be caused by infection or flare-up of the disease. This study aimed to determine whether the ratio of the level of erythrocyte-bound C4d to that of complement receptor 1 (C4d/CR1) can serve as a useful biomarker in the differentiation between infection and flare...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/939783
更新日期:2015-01-01 00:00:00
abstract::Long-term chronic intermittent exposure to altitude hypoxia is a labor phenomenon requiring further research. Using a rat model, we examined whether this type of exposure differed from chronic exposure in terms of pulmonary artery remodeling and other features. Rats were subjected to chronic hypoxia (CH, n = 9) and lo...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/169841
更新日期:2015-01-01 00:00:00
abstract::Ambient assisted living (AAL) aims to help older persons "age-in-place" and manage everyday activities using intelligent and pervasive computing technology. AAL research, however, has yet to explore how AAL might support or collaborate with informal care partners (ICPs), such as relatives and friends, who play importa...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/720483
更新日期:2015-01-01 00:00:00
abstract::Virulence-associated traits have frequently been studied in enterococci and are considered to contribute towards the pathogenicity of infections. In the present study, Enterococcus isolates were collected during diagnostic investigations from meat turkeys in Germany. Twenty-eight isolates of three different Enterococc...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/6147695
更新日期:2019-10-30 00:00:00
abstract::Human cytoplasmic alpha-fetoprotein (AFP) has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA), but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinosi...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/256916
更新日期:2015-01-01 00:00:00
abstract::[This corrects the article DOI: 10.1155/2012/853879.]. ...
journal_title:BioMed research international
pub_type: 已发布勘误
doi:10.1155/2015/292436
更新日期:2015-01-01 00:00:00