Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains.

Abstract:

:Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10-15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues. SymD has proven to be a useful algorithm to detect symmetry. In this paper, we present a new parallelized algorithm called Parallel-SymD for detecting symmetry of proteins on clusters of computers. The achieved speedup of the new Parallel-SymD algorithm scales well with the number of computing processors. Scaling is better for proteins with a larger number of residues. For a protein of 509 residues, a speedup of 63 was achieved on a parallel system with 100 processors.

journal_name

Biomed Res Int

authors

Jha A,Flurchick KM,Bikdash M,Kc DB

doi

10.1155/2016/4628592

subject

Has Abstract

pub_date

2016-01-01 00:00:00

pages

4628592

eissn

2314-6133

issn

2314-6141

journal_volume

2016

pub_type

杂志文章
  • Diethylnitrosamine Increases Proliferation in Early Stages of Hepatic Carcinogenesis in Insulin-Treated Type 1 Diabetic Mice.

    abstract::Diethylnitrosamine (DEN) induces hepatocarcinogenesis, increasing mitotic hepatocytes and leading to chronic inflammation. In addition, type 1 diabetes mellitus (T1DM) is also characterized by a proinflammatory state and by requiring insulin exogenous treatment. Given the association of diabetes, insulin treatment, an...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2018/9472939

    authors: Arboatti AS,Lambertucci F,Sedlmeier MG,Pisani G,Monti J,Álvarez ML,Francés DEA,Ronco MT,Carnovale CE

    更新日期:2018-04-23 00:00:00

  • Inflammation-related effects of diesel engine exhaust particles: studies on lung cells in vitro.

    abstract::Diesel exhaust and its particles (DEP) have been under scrutiny for health effects in humans. In the development of these effects inflammation is regarded as a key process. Overall, in vitro studies report similar DEP-induced changes in markers of inflammation, including cytokines and chemokines, as studies in vivo. I...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2013/685142

    authors: Schwarze PE,Totlandsdal AI,Låg M,Refsnes M,Holme JA,Øvrevik J

    更新日期:2013-01-01 00:00:00

  • The Bewildering Effect of AMPK Activators in Alzheimer's Disease: Review of the Current Evidence.

    abstract::Alzheimer's disease is a multifactorial neurodegenerative disease characterized by progressive cognitive dysfunction. It is the most common form of dementia. The pathologic hallmarks of the disease include extracellular amyloid plaque, intracellular neurofibrillary tangles, and oxidative stress, to mention some of the...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2020/9895121

    authors: Assefa BT,Tafere GG,Wondafrash DZ,Gidey MT

    更新日期:2020-02-18 00:00:00

  • Regulatory systems in bone marrow for hematopoietic stem/progenitor cells mobilization and homing.

    abstract::Regulation of hematopoietic stem cell release, migration, and homing from the bone marrow (BM) and of the mobilization pathway involves a complex interaction among adhesion molecules, cytokines, proteolytic enzymes, stromal cells, and hematopoietic cells. The identification of new mechanisms that regulate the traffick...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2013/312656

    authors: Alvarez P,Carrillo E,Vélez C,Hita-Contreras F,Martínez-Amat A,Rodríguez-Serrano F,Boulaiz H,Ortiz R,Melguizo C,Prados J,Aránega A

    更新日期:2013-01-01 00:00:00

  • T Helper Lymphocyte Subsets and Plasticity in Autoimmunity and Cancer: An Overview.

    abstract::In response to cytokine signalling and other factors, CD4-positive T lymphocytes differentiate into distinct populations that are characterized by the production of certain cytokines and are controlled by different master transcription factors. The spectrum of such populations, which was initially limited to Th1 and T...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/327470

    authors: Ivanova EA,Orekhov AN

    更新日期:2015-01-01 00:00:00

  • Potential Relationship between Clinical Significance and Serum Exosomal miRNAs in Patients with Multiple Myeloma.

    abstract::This study evaluated the potential relationship between exosomal miRNAs and clinical symptoms in patients with multiple myeloma (MM). Forty-eight newly diagnosed myeloma patients and sixteen normal donors were enrolled in the study. The results showed that the relative expression levels of let-7c-5p, let-7d-5p, miR-14...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/1575468

    authors: Zhang ZY,Li YC,Geng CY,Wang HJ,Chen WM

    更新日期:2019-12-14 00:00:00

  • The Diagnostic Value of Quantitative CT Analysis of Ground-Glass Volume Percentage in Differentiating Epidermal Growth Factor Receptor Mutation and Subtypes in Lung Adenocarcinoma.

    abstract:Objective:To retrospectively investigate computed tomographic (CT) quantitative analysis of ground-glass opacity (GGO) volume percentage and morphologic features of resected lung adenocarcinomas according to epidermal growth factor receptor (EGFR) mutation status and subtypes. Methods:Amplification refractory mutation...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/9643836

    authors: Wang H,Guo H,Wang Z,Shan B,Lin J

    更新日期:2019-03-06 00:00:00

  • A Review of NEPA, a Novel Fixed Antiemetic Combination with the Potential for Enhancing Guideline Adherence and Improving Control of Chemotherapy-Induced Nausea and Vomiting.

    abstract::Combination antiemetic regimens targeting multiple molecular pathways associated with emesis have become the standard of care for prevention of chemotherapy-induced nausea and vomiting (CINV) related to highly and moderately emetogenic chemotherapies. Antiemetic consensus guidelines from several professional societies...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/651879

    authors: Hesketh PJ,Aapro M,Jordan K,Schwartzberg L,Bosnjak S,Rugo H

    更新日期:2015-01-01 00:00:00

  • Tracking Transplanted Stem Cells Using Magnetic Resonance Imaging and the Nanoparticle Labeling Method in Urology.

    abstract::A reliable in vivo imaging method to localize transplanted cells and monitor their viability would enable a systematic investigation of cell therapy. Most stem cell transplantation studies have used immunohistological staining, which does not provide information about the migration of transplanted cells in vivo in the...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/231805

    authors: Kim JH,Lee HJ,Song YS

    更新日期:2015-01-01 00:00:00

  • Prognostic Role of Left Ventricular Systolic Function Measured by Speckle Tracking Echocardiography in Septic Shock.

    abstract:Background:Left ventricular (LV) systolic dysfunction is common in septic shock. Global longitudinal strain (GLS) measured by speckle tracking echocardiography (STE) is a useful marker of intrinsic left ventricular systolic function. However, the association between left ventricular GLS and outcome in septic patients i...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/7927353

    authors: Hai PD,Binh NT,Hien NVQ,Hoang NH,Hoan VN,Son PN,Hoa LTV

    更新日期:2020-10-21 00:00:00

  • Differentiation of Human Amniotic Mesenchymal Stem Cells into Human Anterior Cruciate Ligament Fibroblast Cells by In Vitro Coculture.

    abstract::Anterior cruciate ligament injuries are common in humans, though cellular components of the knee have little regenerative or proliferation potential. This study investigated the differentiation of human amnion-derived mesenchymal stem cells (hAMSCs) into human anterior cruciate ligament fibroblasts (hACLFs) in vitro t...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2017/7360354

    authors: Li Y,Liu Z,Jin Y,Zhu X,Wang S,Yang J,Ren Y,Fu Q,Xiong H,Zou G,Liu Y

    更新日期:2017-01-01 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

  • Innovative strategies to overcome biofilm resistance.

    abstract::We review the recent literature concerning the efficiency of antimicrobial photodynamic inactivation toward various microbial species in planktonic and biofilm cultures. The review is mainly focused on biofilm-growing microrganisms because this form of growth poses a threat to chronically infected or immunocompromised...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2013/150653

    authors: Taraszkiewicz A,Fila G,Grinholc M,Nakonieczna J

    更新日期:2013-01-01 00:00:00

  • Impact of Radiofrequency Ablation and Antiarrhythmic Medications on the Quality of Life of Patients with Supraventricular Tachycardias: Preliminary Validation of the Greek Version of the Umea22 (U22) Questionnaire.

    abstract:Objective:This study aims to (i) translate, culturally adapt, and preliminarily validate the arrhythmia-specific Umea22 (U22) questionnaire and (ii) assess the impact of radiofrequency (RF) ablation and medical treatment on the quality of life of patients with supraventricular tachycardias (SVTs). Methods:A total of 1...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2018/3059478

    authors: Domeyer PR,Giannakidou SC,Kyriakou P,Katsari V,Antoniadis AP,Lagos IK,Fragakis N,Varaklioti A,Vassilikos VP

    更新日期:2018-10-09 00:00:00

  • A therapeutic strategy for spinal cord defect: human dental follicle cells combined with aligned PCL/PLGA electrospun material.

    abstract::Stem cell implantation has been utilized for the repair of spinal cord injury; however, it shows unsatisfactory performance in repairing large scale lesion of an organ. We hypothesized that dental follicle cells (DFCs), which possess multipotential capability, could reconstruct spinal cord defect (SCD) in combination ...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/197183

    authors: Li X,Yang C,Li L,Xiong J,Xie L,Yang B,Yu M,Feng L,Jiang Z,Guo W,Tian W

    更新日期:2015-01-01 00:00:00

  • Effects of Platelet-Rich Plasma on Proliferation, Viability, and Odontogenic Differentiation of Neural Crest Stem-Like Cells Derived from Human Dental Apical Papilla.

    abstract:Objective:This study is aimed at evaluating the effects of platelet-rich plasma (PRP) on proliferation, viability, and odontogenic differentiation of neural crest stem-like cells (NCSCs) derived from human dental apical papilla. Materials and Methods:Cells from apical papillae were obtained and then induced to form ne...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/4671989

    authors: Li J,Xiang L,Guan C,Yang X,Hu X,Zhang X,Zhang W

    更新日期:2020-05-09 00:00:00

  • A Novel Seventeen-Gene Metabolic Signature for Predicting Prognosis in Colon Cancer.

    abstract::A metabolic disorder is considered one of the hallmarks of cancer. Multiple differentially expressed metabolic genes have been identified in colon cancer (CC), and their biological functions and prognostic values have been well explored. The purpose of the present study was to establish a metabolic signature to optimi...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/4845360

    authors: Luo D,Shan Z,Liu Q,Cai S,Li Q,Li X

    更新日期:2020-11-17 00:00:00

  • Atypical enteropathogenic Escherichia coli strains form biofilm on abiotic surfaces regardless of their adherence pattern on cultured epithelial cells.

    abstract::The aim of this study was to determine the capacity of biofilm formation of atypical enteropathogenic Escherichia coli (aEPEC) strains on abiotic and biotic surfaces. Ninety-one aEPEC strains, isolated from feces of children with diarrhea, were analyzed by the crystal violet (CV) assay on an abiotic surface after 24 h...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/845147

    authors: Culler HF,Mota CM,Abe CM,Elias WP,Sircili MP,Franzolin MR

    更新日期:2014-01-01 00:00:00

  • Aesthetic evaluation of the nasolabial region in children with unilateral cleft lip and palate comparing expert versus nonexperience health professionals.

    abstract::Esthetic evaluation of cleft lip and palate rehabilitation outcomes may assist in the determination of new surgical interventions and aid in reevaluation of treatment protocols. Our objective was to compare esthetics assessments of the nasolabial region in children with a unilateral cleft lip and palate between health...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/460106

    authors: Paiva TS,Andre M,Paiva WS,Mattos BS

    更新日期:2014-01-01 00:00:00

  • Prokineticin 2 upregulation in the peripheral nervous system has a major role in triggering and maintaining neuropathic pain in the chronic constriction injury model.

    abstract::The new chemokine Prokineticin 2 (PROK2) and its receptors (PKR1 and PKR2) have a role in inflammatory pain and immunomodulation. Here we identified PROK2 as a critical mediator of neuropathic pain in the chronic constriction injury (CCI) of the sciatic nerve in mice and demonstrated that blocking the prokineticin rec...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/301292

    authors: Lattanzi R,Maftei D,Marconi V,Florenzano F,Franchi S,Borsani E,Rodella LF,Balboni G,Salvadori S,Sacerdote P,Negri L

    更新日期:2015-01-01 00:00:00

  • Health Effects of 12 Weeks of Team-Sport Training and Fitness Training in a Community Health Centre for Sedentary Men with Lifestyle Diseases.

    abstract::This study compares the effects of team-sport training, for sedentary men with lifestyle diseases, with fitness training in a pragmatic set-up in a community health centre (CHC). Thirty-two men in the fitness group (FiG) and 36 men in the team-sport group (TsG) completed the training and trained for 60-90 min, two tim...

    journal_title:BioMed research international

    pub_type: 临床试验,杂志文章

    doi:10.1155/2018/1571807

    authors: Møller TK,Nielsen TT,Andersen R,Lundager I,Hansen HF,Ottesen L,Krustrup P,Randers MB

    更新日期:2018-05-15 00:00:00

  • Prevalence of anaemia among pregnant women at booking in the University of Uyo Teaching Hospital, Uyo, Nigeria.

    abstract:BACKGROUND:Anaemia with an estimated prevalence of 35-75% among pregnant women is a major cause of maternal deaths in Nigeria. objective: To determine the prevalence of anaemia, associated sociodemographic factors and red cell morphological pattern among pregnant women during booking at the University Teaching Hospital...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/849080

    authors: Olatunbosun OA,Abasiattai AM,Bassey EA,James RS,Ibanga G,Morgan A

    更新日期:2014-01-01 00:00:00

  • Synthesis and anticancer activity of N-aryl-5-substituted-1,3,4-oxadiazol-2-amine analogues.

    abstract::In continuance of our search for anticancer agents, we report herein the synthesis and anticancer activity of some novel oxadiazole analogues. The compounds were screened for anticancer activity as per National Cancer Institute (NCI US) protocol on leukemia, melanoma, lung, colon, CNS, ovarian, renal, prostate, and br...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/814984

    authors: Ahsan MJ,Sharma J,Singh M,Jadav SS,Yasmin S

    更新日期:2014-01-01 00:00:00

  • A low-dose combination of fluvastatin and valsartan: a new "drug" and a new approach for decreasing the arterial age.

    abstract::We have developed a new "drug" and approach that appear to be effective in reducing arterial age. This "drug" represents a low, subtherapeutic dose of statin and sartan and particularly their low-dose combination. The improvement of arterial wall characteristics, also reflecting in a decrease of arterial age, was achi...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/235709

    authors: Janić M,Lunder M,Šabovič M

    更新日期:2015-01-01 00:00:00

  • Potential Anticancer Mechanisms of a Novel EGFR/DNA-Targeting Combi-Molecule (JDF12) against DU145 Prostate Cancer Cells: An iTRAQ-Based Proteomic Analysis.

    abstract::The development of multitargeting drugs is an emerging trend in cancer research. To promote further development and clinical application of multitargeting drugs, this research was performed. MTT assay and flow cytometry of Annexin V/propidium iodide staining were used to confirm the proapoptotic efficacy of a novel co...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2017/8050313

    authors: Zheng H,Liang G,Chen Y,Lin S,Liu W,Fang Y

    更新日期:2017-01-01 00:00:00

  • Characterization of multiwalled carbon nanotube-reinforced hydroxyapatite composites consolidated by spark plasma sintering.

    abstract::Pure HA and 1, 3, 5, and 10 vol% multiwalled carbon nanotube- (MWNT-) reinforced hydroxyapatite (HA) were consolidated using a spark plasma sintering (SPS) technique. The relative density of pure HA increased with increasing sintering temperature, but that of the MWNT/HA composite reached almost full density at 900°C,...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/768254

    authors: Kim DY,Han YH,Lee JH,Kang IK,Jang BK,Kim S

    更新日期:2014-01-01 00:00:00

  • Mitochondrial Dysfunction and Autophagy in Hepatic Ischemia/Reperfusion Injury.

    abstract::Ischemia/reperfusion (I/R) injury remains a major complication of liver resection, transplantation, and hemorrhagic shock. Although the mechanisms that contribute to hepatic I/R are complex and diverse involving the interaction of cell injury in hepatocytes, immune cells, and endothelium, mitochondrial dysfunction is ...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/183469

    authors: Go KL,Lee S,Zendejas I,Behrns KE,Kim JS

    更新日期:2015-01-01 00:00:00

  • Angiopoietin-1 Promotes the Integrity of Neovascularization in the Subcutaneous Matrigel of Type 1 Diabetic Rats.

    abstract:Objective:This study aimed to investigate the effects of Ang-1 on neovascularization of diabetic organs by subcutaneous Matrigel angiogenesis model, established in type 1 diabetic rats. Methods:Ang-1 adenoviral vector was constructed. The rat model was established by STZ and divided into four group. The Matrigel was i...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/2016972

    authors: Li S,Zou H,Gong M,Chen Y,Yan X,Yu L,Yang Y

    更新日期:2019-01-09 00:00:00

  • Durable Mechanical Circulatory Support versus Organ Transplantation: Past, Present, and Future.

    abstract::For more than 30 years, heart transplantation has been a successful therapy for patients with terminal heart failure. Mechanical circulatory support (MCS) was developed as a therapy for end-stage heart failure at a time when cardiac transplantation was not yet a useful treatment modality. With the more successful outc...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/849571

    authors: Anand J,Singh SK,Antoun DG,Cohn WE,Frazier OH,Mallidi HR

    更新日期:2015-01-01 00:00:00

  • 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