Mixing energy models in genetic algorithms for on-lattice protein structure prediction.

Abstract:

:Protein structure prediction (PSP) is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is not clearly known. A high resolution 20 × 20 energy model could better capture the behaviour of the actual energy function than a low resolution energy model such as hydrophobic polar. However, the fine grained details of the high resolution interaction energy matrix are often not very informative for guiding the search. In contrast, a low resolution energy model could effectively bias the search towards certain promising directions. In this paper, we develop a genetic algorithm that mainly uses a high resolution energy model for protein structure evaluation but uses a low resolution HP energy model in focussing the search towards exploring structures that have hydrophobic cores. We experimentally show that this mixing of energy models leads to significant lower energy structures compared to the state-of-the-art results.

journal_name

Biomed Res Int

authors

Rashid MA,Newton MA,Hoque MT,Sattar A

doi

10.1155/2013/924137

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

924137

eissn

2314-6133

issn

2314-6141

journal_volume

2013

pub_type

杂志文章
  • mTOR in viral hepatitis and hepatocellular carcinoma: function and treatment.

    abstract::As the fifth most common cancer in men and the eighth most common cancer in women, hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide, with standard chemotherapy and radiation being minimally effective in prolonging survival. Virus hepatitis, particularly HBV and HCV infection is th...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2014/735672

    authors: Wang Z,Jin W,Jin H,Wang X

    更新日期:2014-01-01 00:00:00

  • MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.

    abstract::The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most of these publically available RNA-Seq studies are d...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/318064

    authors: Kumar P,Halama A,Hayat S,Billing AM,Gupta M,Yousri NA,Smith GM,Suhre K

    更新日期:2015-01-01 00:00:00

  • 18F-labeling using click cycloadditions.

    abstract::Due to expanding applications of positron emission tomography (PET) there is a demand for developing new techniques to introduce fluorine-18 (t 1/2 = 109.8 min). Considering that most novel PET tracers are sensitive biomolecules and that direct introduction of fluorine-18 often needs harsh conditions, the insertion of...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2014/361329

    authors: Kettenbach K,Schieferstein H,Ross TL

    更新日期:2014-01-01 00:00:00

  • LncRNA BLACAT1 May Serve as a Prognostic Predictor in Cancer: Evidence from a Meta-Analysis.

    abstract:Background:As a newly discovered lncRNA, bladder cancer-associated transcript 1 (BLACAT1) has been reported to correlate with poor clinical outcomes in several different cancers. This study aimed to evaluate its generalized predictive value for cancer prognosis. Materials and Methods:We thoroughly searched PubMed, Emb...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2019/1275491

    authors: Lu H,Liu H,Yang X,Ye T,Lv P,Wu X,Ye Z

    更新日期:2019-04-02 00:00:00

  • EEG Recording and Online Signal Processing on Android: A Multiapp Framework for Brain-Computer Interfaces on Smartphone.

    abstract:Objective:Our aim was the development and validation of a modular signal processing and classification application enabling online electroencephalography (EEG) signal processing on off-the-shelf mobile Android devices. The software application SCALA (Signal ProCessing and CLassification on Android) supports a standardi...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2017/3072870

    authors: Blum S,Debener S,Emkes R,Volkening N,Fudickar S,Bleichner MG

    更新日期:2017-01-01 00:00:00

  • Different Genotype Distribution of Human Papillomavirus between Cervical and Esophageal Cancers: A Study in Both High-Incidence Areas, Xinjiang, China.

    abstract::The aim of this study is to reveal the certain human papillomavirus (HPV) genotype distribution between cervical cancer and esophageal cancer in the both high-incidence geographic regions. For this study, we collected and detected the infection of HPV in 120 paraffin-embedded esophageal tissues and 152 paraffin-embedd...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/7926754

    authors: Zheng Y,Fan Y,Zeng Y,Liu S,Gao L

    更新日期:2020-12-02 00:00:00

  • Neuroinflammatory Gene Expression Pattern Is Similar between Allergic Rhinitis and Atopic Dermatitis but Distinct from Atopic Asthma.

    abstract:Methods:In the study, we included 86 children diagnosed with atopic asthma (n = 25), allergic rhinitis (n = 20), and atopic dermatitis (n = 20) and healthy control subjects (n = 21) of Caucasian origin from the Polish population. The blood leukocyte expression of 31 genes involved in neuroinflammatory response (neurotr...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/7196981

    authors: Sobkowiak P,Langwiński W,Nowakowska J,Wojsyk-Banaszak I,Szczepankiewicz D,Jenerowicz D,Wasilewska E,Bręborowicz A,Szczepankiewicz A

    更新日期:2020-06-10 00:00:00

  • A 12-Week Assessment of the Treatment of White Spot Lesions with CPP-ACP Paste and/or Fluoride Varnish.

    abstract::This 12-week clinical study evaluated the impact of 10% CPP-ACP and 5% sodium fluoride varnish regimes on the regression of nonorthodontic white spot lesions (WSLs). The study included 21 children with 101 WSLs who were randomised into four treatment regimes: weekly clinical applications of fluoride varnish for the fi...

    journal_title:BioMed research international

    pub_type: 杂志文章,随机对照试验

    doi:10.1155/2016/8357621

    authors: Güçlü ZA,Alaçam A,Coleman NJ

    更新日期:2016-01-01 00:00:00

  • Germacrone Inhibits Cell Proliferation and Induces Apoptosis in Human Esophageal Squamous Cell Carcinoma Cells.

    abstract::Germacrone, a natural 10-membered monocyclic sesquiterpene with three double bonds and a ketone, was isolated from the roots of traditional Chinese medicine Saussurea costus (SC). The pharmacological value and intrinsic mechanism of germacrone in the treatment of esophageal squamous cell carcinoma (ESCC) are still unc...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/7643248

    authors: Zhang R,Hao J,Guo K,Liu W,Yao F,Wu Q,Liu C,Wang Q,Yang X

    更新日期:2020-01-30 00:00:00

  • Recent Advances in HBV Reactivation Research.

    abstract::Hepatitis B virus (HBV) is an important public health problem that poses a serious threat to human health. HBV reactivation generally occurs in overt or occult HBV infection patients who suffered DDAs, chemotherapy, or immunosuppressive therapy, especially when some solid tumors and leukemia patients are using hormone...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2018/2931402

    authors: Guo L,Wang D,Ouyang X,Tang N,Chen X,Zhang Y,Zhu H,Li X

    更新日期:2018-12-26 00:00:00

  • Functions of the C2H2 Transcription Factor Gene thmea1 in Trichoderma harzianum under Copper Stress Based on Transcriptome Analysis.

    abstract::Trichoderma spp. are important biocontrol filamentous fungi and have tremendous potential in soil bioremediation. In our previous studies, a C2H2 type transcription factor coding gene (thmea1) was cloned from a biocontrol agent T. harzianum Th-33; the encoded sequence of thmea1 contained 3 conserved C2H2 domains with ...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2018/8149682

    authors: Mei J,Wang L,Jiang X,Wu B,Li M

    更新日期:2018-07-18 00:00:00

  • Pediatric tuberculosis in young children in India: a prospective study.

    abstract:BACKGROUND:India has one of the highest tuberculosis (TB) burdens globally. However, few studies have focused on TB in young children, a vulnerable population, where lack of early diagnosis results in poor outcomes. METHODS:Young children (≤ 5 years) with suspected TB were prospectively enrolled at a tertiary hospital...

    journal_title:BioMed research international

    pub_type: 临床试验,杂志文章

    doi:10.1155/2013/783698

    authors: Jain SK,Ordonez A,Kinikar A,Gupte N,Thakar M,Mave V,Jubulis J,Dharmshale S,Desai S,Hatolkar S,Kagal A,Lalvani A,Gupta A,Bharadwaj R

    更新日期:2013-01-01 00:00:00

  • Radiopharmaceutical stem cell tracking for neurological diseases.

    abstract::Although neurological ailments continue to be some of the main causes of disease burden in the world, current therapies such as pharmacological agents have limited potential in the restoration of neural functions. Cell therapies, firstly applied to treat different hematological diseases, are now being investigated in ...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2014/417091

    authors: Rosado-de-Castro PH,Pimentel-Coelho PM,Gutfilen B,Lopes de Souza SA,de Freitas GR,Mendez-Otero R,Barbosa da Fonseca LM

    更新日期:2014-01-01 00:00:00

  • Molecular characterization and screening for sheath blight resistance using Malaysian isolates of Rhizoctonia solani.

    abstract::Two field isolates of Rhizoctonia solani were isolated from infected paddy plants in Malaysia. These isolates were verified via ITS-rDNA analysis that yielded ~720 bp products of the ITS1-5.8S-ITS4 region, respectively. The sequenced products showed insertion and substitution incidences which may result in strain dive...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/434257

    authors: Nadarajah K,Omar NS,Rosli MM,Shin Tze O

    更新日期:2014-01-01 00:00:00

  • Relation between the Sensory and Anthropometric Variables in the Quiet Standing Postural Control: Is the Inverted Pendulum Important for the Static Balance Control?

    abstract:UNLABELLED:The aim of this study was to evaluate the relation between the sensory and anthropometric variables in the quiet standing. METHODS:One hundred individuals (50 men, 50 women; 20-40 years old) participated in this study. For all participants, the body composition (fat tissue, lean mass, bone mineral content, ...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/985312

    authors: Alonso AC,Mochizuki L,Silva Luna NM,Ayama S,Canonica AC,Greve JM

    更新日期:2015-01-01 00:00:00

  • The Assessment of Oral Microflora Exposed to 3% Ethanolic Extract of Brazilian Green Propolis Preparation Used for Hygiene Maintenance following Minor Oral Surgeries.

    abstract::The aim of this study was to investigate the influence of a topically administered hygienic preparation containing a 3% ethanolic extract of Brazilian green propolis (EEP-B) on oral microflora spectrum changes in a group of patients who underwent common oral surgery procedures. Two gel samples were compared: the teste...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/869575

    authors: Morawiec T,Mertas A,Wojtyczka RD,Niedzielska I,Dziedzic A,Bubiłek-Bogacz A,Sender J,Wróbel J,Tanasiewicz M,Wesołowski P,Król W

    更新日期:2015-01-01 00:00:00

  • Medication Adherence Measures: An Overview.

    abstract::WHO reported that adherence among patients with chronic diseases averages only 50% in developed countries. This is recognized as a significant public health issue, since medication nonadherence leads to poor health outcomes and increased healthcare costs. Improving medication adherence is, therefore, crucial and revea...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/217047

    authors: Lam WY,Fresco P

    更新日期:2015-01-01 00:00:00

  • HMGB1-Induced Cross Talk between PTEN and miRs 221/222 in Thyroid Cancer.

    abstract::High mobility group box 1 (HMGB1) is an ubiquitous protein that plays different roles in the nucleus, cytoplasm, and extracellular space. It is an important DAMP molecule that allows communication between damaged or tumor cells and the immune system. Tumor cells exploit HMGB1's ability to activate intracellular pathwa...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/512027

    authors: Mardente S,Mari E,Massimi I,Fico F,Faggioni A,Pulcinelli F,Antonaci A,Zicari A

    更新日期:2015-01-01 00:00:00

  • The influence of simulated microgravity on purinergic signaling is different between individual culture and endothelial and smooth muscle cell coculture.

    abstract::Exposure to microgravity conditions causes cardiovascular deconditioning in astronauts during spaceflight. Until now, no specific drugs are available for countermeasure, since the underlying mechanism is largely unknown. Endothelial cells (ECs) and smooth muscle cells (SMCs) play key roles in various vascular function...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/413708

    authors: Zhang Y,Lau P,Pansky A,Kassack M,Hemmersbach R,Tobiasch E

    更新日期:2014-01-01 00:00:00

  • Onlay Repair Technique for the Management of Ureteral Strictures: A Comprehensive Review.

    abstract::Ureteroplasty using onlay grafts or flaps emerged as an innovative procedure for the management of proximal and midureteral strictures. Autologous grafts or flaps used commonly in ureteroplasty include the oral mucosae, bladder mucosae, ileal mucosae, and appendiceal mucosae. Oral mucosa grafts, especially buccal muco...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2020/6178286

    authors: Xiong S,Wang J,Zhu W,Yang K,Ding G,Li X,Eun DD

    更新日期:2020-07-27 00:00:00

  • Association between ELABELA Serum Concentrations in First Trimester and Pregnancy-Induced Hypertension.

    abstract::ELABELA (ELA) is considered to be implicated in the pathophysiology of preeclampsia (PE), since ELA-deficient mice exhibited PE-like symptoms and infusion of exogenous ELA normalized the gestational hypertension (GH) and proteinuria. However, no evidence show that circulating ELA is deficient in early placental develo...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/2051701

    authors: Ma S,Guo C,Zhang J,Long S,Tan H,You Y

    更新日期:2020-09-28 00:00:00

  • Postsurgical pathologies associated with intradural electrical stimulation in the central nervous system: design implications for a new clinical device.

    abstract::Spinal cord stimulation has been utilized for decades in the treatment of numerous conditions such as failed back surgery and phantom limb syndromes, arachnoiditis, cancer pain, and others. The placement of the stimulating electrode array was originally subdural but, to minimize surgical complexity and reduce the risk...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2014/989175

    authors: Gibson-Corley KN,Flouty O,Oya H,Gillies GT,Howard MA

    更新日期:2014-01-01 00:00:00

  • Cigarette Smoke Induced Lung Barrier Dysfunction, EMT, and Tissue Remodeling: A Possible Link between COPD and Lung Cancer.

    abstract::Chronic obstructive pulmonary disease (COPD) and lung cancer, closely related to smoking, are major lung diseases affecting millions of individuals worldwide. The generated gas mixture of smoking is proved to contain about 4,500 components such as carbon monoxide, nicotine, oxidants, fine particulate matter, and aldeh...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2019/2025636

    authors: Hou W,Hu S,Li C,Ma H,Wang Q,Meng G,Guo T,Zhang J

    更新日期:2019-06-24 00:00:00

  • Individual IOL surface topography analysis by the WaveMaster Reflex UV.

    abstract:PURPOSE:In order to establish inspection routines for individual intraocular lenses (IOLs), their surfaces have to be measured separately. Currently available measurement devices lack this functionality. The purpose of this study is to evaluate a new topography measurement device based on wavefront analysis for measuri...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2013/363742

    authors: Kannengießer M,Langenbucher A,Janunts E

    更新日期:2013-01-01 00:00:00

  • Alteration of Angiopoietin-Like Protein 4 Levels in Serum or Urine Correlate with Different Biochemical Markers in Hyperlipidemia-Related Proteinuria.

    abstract::Angiopoietin-like protein 4 (ANGPTL4) is widely known as a key regulator of lipid metabolism. We investigated the relationship between ANGPTL4 expression in serum or urine and blood lipid or urine protein levels of patients with hyperlipidemia- (HL-) related proteinuria. Sixty-eight patients with HL-related proteinuri...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/5281251

    authors: Gao X,Zhang M,Feng W,Xu Z,Wang Y,Shi L,Zhang J

    更新日期:2020-03-23 00:00:00

  • Intake of Meals Containing High Levels of Carbohydrates or High Levels of Unsaturated Fatty Acids Induces Postprandial Dysmetabolism in Young Overweight/Obese Men.

    abstract::Postprandial metabolic response depends on the meals' components and can be different in normal weight and obese people. However, there are some discrepancies between various reports. The aim of this study was to determine the metabolic response after intake of standardised meals with various fat and carbohydrate cont...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/147196

    authors: Adamska E,Ostrowska L,Gościk J,Waszczeniuk M,Krętowski A,Górska M

    更新日期:2015-01-01 00:00:00

  • Mice Selected for Acute Inflammation Present Altered Immune Response during Pristane-Induced Arthritis Progression.

    abstract::Mouse lines selected for maximal (AIRmax) or minimal acute inflammatory reaction (AIRmin) were used to characterize the immune response and the influence of genetic background during pristane-induced arthritis (PIA). Susceptible AIRmax mice demonstrated exacerbated cellular profiles during PIA, with intense infiltrati...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2018/1267038

    authors: Correa MA,Borrego A,Jensen JR,Cabrera WHK,Barros M,Katz ISS,Canhamero T,Spadafora-Ferreira M,Fernandes JG,Starobinas N,Ribeiro OG,Ibañez OM,De Franco M

    更新日期:2018-10-08 00:00:00

  • Posttransplant Anemia as a Prognostic Factor of Mortality in Kidney-Transplant Recipients.

    abstract::Background. Findings on the association between posttransplant anemia (PTA) and mortality in posttransplant patients are scarce. This study explored whether PTA shortly after kidney transplantation (KT) predicts mortality at up to 10 years' follow-up, stratified for chronic kidney disease (CKD) stages. Methods. PTA wa...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2017/6987240

    authors: Majernikova M,Rosenberger J,Prihodova L,Jarcuskova M,Roland R,Groothoff JW,van Dijk JP

    更新日期:2017-01-01 00:00:00

  • GAS1 Deficient Enhances UPR Activity in Saccharomyces cerevisiae.

    abstract::Beta-1,3-glucanosyltransferase (Gas1p) plays important roles in cell wall biosynthesis and morphogenesis and has been implicated in DNA damage responses and cell cycle regulation in fungi. Yeast Gas1p has also been reported to participate in endoplasmic reticulum (ER) stress responses. However, the precise roles and m...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/1238581

    authors: Cui HJ,Cui XG,Jing X,Yuan Y,Chen YQ,Sun YX,Zhao W,Liu XG

    更新日期:2019-06-02 00:00:00

  • Regulation of ICAM-1 in cells of the monocyte/macrophage system in microgravity.

    abstract::Cells of the immune system are highly sensitive to altered gravity, and the monocyte as well as the macrophage function is proven to be impaired under microgravity conditions. In our study, we investigated the surface expression of ICAM-1 protein and expression of ICAM-1 mRNA in cells of the monocyte/macrophage system...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/538786

    authors: Paulsen K,Tauber S,Dumrese C,Bradacs G,Simmet DM,Gölz N,Hauschild S,Raig C,Engeli S,Gutewort A,Hürlimann E,Biskup J,Unverdorben F,Rieder G,Hofmänner D,Mutschler L,Krammer S,Buttron I,Philpot C,Huge A,Lier H,Barz

    更新日期:2015-01-01 00:00:00