当前位置： SCI文献检索 > Biomed Research International期刊下所有文献 > An accurate method for prediction of protein-ligand binding site on protein surface using SVM and statistical depth function.

An accurate method for prediction of protein-ligand binding site on protein surface using SVM and statistical depth function.

Abstract：

:Since proteins carry out their functions through interactions with other molecules, accurately identifying the protein-ligand binding site plays an important role in protein functional annotation and rational drug discovery. In the past two decades, a lot of algorithms were present to predict the protein-ligand binding site. In this paper, we introduce statistical depth function to define negative samples and propose an SVM-based method which integrates sequence and structural information to predict binding site. The results show that the present method performs better than the existent ones. The accuracy, sensitivity, and specificity on training set are 77.55%, 56.15%, and 87.96%, respectively; on the independent test set, the accuracy, sensitivity, and specificity are 80.36%, 53.53%, and 92.38%, respectively.

journal_name

Biomed Res Int

journal_title

BioMed research international

authors

Wang K,Gao J,Shen S,Tuszynski JA,Ruan J,Hu G

doi

10.1155/2013/409658

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

409658

eissn

2314-6133

issn

2314-6141

journal_volume

2013

pub_type

杂志文章

相关文献

Biomed Research International文献大全
  • High glucose induces sumoylation of Smad4 via SUMO2/3 in mesangial cells.

    abstract：:Recent studies have shown that sumoylation is a posttranslational modification involved in regulation of the transforming growth factor-β (TGF-β) signaling pathway, which plays a critical role in renal fibrosis in diabetic nephropathy (DN). However, the role of sumoylation in the regulation of TGF-β signaling in DN is...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2014/782625

    authors： Zhou X,Gao C,Huang W,Yang M,Chen G,Jiang L,Gou F,Feng H,Ai N,Xu Y

    更新日期：2014-01-01 00:00:00

  • Automatic Segmentation of Ultrasound Tomography Image.

    abstract：:Ultrasound tomography (UST) image segmentation is fundamental in breast density estimation, medicine response analysis, and anatomical change quantification. Existing methods are time consuming and require massive manual interaction. To address these issues, an automatic algorithm based on GrabCut (AUGC) is proposed i...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2017/2059036

    authors： Wu S,Yu S,Zhuang L,Wei X,Sak M,Duric N,Hu J,Xie Y

    更新日期：2017-01-01 00:00:00

  • Immunoregulation of Bone Marrow-Derived Mesenchymal Stem Cells on the Chronic Cigarette Smoking-Induced Lung Inflammation in Rats.

    abstract：:Impact of bone mesenchymal stem cell (BMSC) transfusion on chronic smoking-induced lung inflammation is poorly understood. In this study, a rat model of smoking-related lung injury was induced and the rats were treated with vehicle or BMSCs for two weeks. Different subsets of CD4+ T cells, cytokines, and anti-elastin ...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2015/932923

    authors： Li X,Wang J,Cao J,Ma L,Xu J

    更新日期：2015-01-01 00:00:00

  • A Prospective Noninterventional, Observational Study to Describe the Effectiveness and Safety of Trandolapril and Verapamil Single-Pill Combination in the Management of Patients with Hypertension and Type 2 Diabetes Mellitus: A Harvest TR Study.

    abstract：:Maintaining regular blood pressure control usually requires multidrug regimens rather than monotherapy. The objective of this study was to describe the effectiveness and safety of an angiotensin-converting enzyme inhibitor and a nondihydropyridine calcium channel blocker in a single-tablet combination in patients with...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2020/2123601

    authors： Atalar E,Eskin F,Tugtekin HB,Karabulut A,Kanyilmaz S,Kirbiyik H,Ozyildiz AG

    更新日期：2020-09-05 00:00:00

  • Tumor initiating cells and chemoresistance: which is the best strategy to target colon cancer stem cells?

    abstract：:There is an emerging body of evidence that chemoresistance and minimal residual disease result from selective resistance of a cell subpopulation from the original tumor that is molecularly and phenotypically distinct. These cells are called "cancer stem cells" (CSCs). In this review, we analyze the potential targeting...

    journal_title：BioMed research international

    pub_type： 杂志文章,评审

    doi：10.1155/2014/859871

    authors： Paldino E,Tesori V,Casalbore P,Gasbarrini A,Puglisi MA

    更新日期：2014-01-01 00:00:00

  • The Effect of Omega-3 Docosahexaenoic Acid Supplementation on Gestational Length: Randomized Trial of Supplementation Compared to Nutrition Education for Increasing n-3 Intake from Foods.

    abstract：OBJECTIVE:DHA supplementation was compared to nutrition education to increase DHA consumption from fish and DHA fortified foods. DESIGN:This two-part intervention included a randomized double-blind placebo controlled DHA supplementation arm and a nutrition education arm designed to increase intake of DHA from dietary ...

    journal_title：BioMed research international

    pub_type： 杂志文章,随机对照试验

    doi：10.1155/2015/123078

    authors： Harris MA,Reece MS,McGregor JA,Wilson JW,Burke SM,Wheeler M,Anderson JE,Auld GW,French JI,Allen KG

    更新日期：2015-01-01 00:00:00

  • Lack of association between JAK3 gene polymorphisms and cardiovascular disease in Spanish patients with rheumatoid arthritis.

    abstract：:Rheumatoid arthritis (RA) is a polygenic disease associated with accelerated atherosclerosis and increased cardiovascular (CV) mortality. JAK/STAT signalling pathway is involved in autoimmune diseases and in the atherosclerotic process. JAK3 is a highly promising target for immunomodulatory drugs and polymorphisms in ...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2015/318364

    authors： García-Bermúdez M,López-Mejías R,Genre F,Castañeda S,Corrales A,Llorca J,González-Juanatey C,Ubilla B,Miranda-Filloy JA,Pina T,Gómez-Vaquero C,Rodríguez-Rodríguez L,Fernández-Gutiérrez B,Balsa A,Pascual-Salcedo D,López-Long

    更新日期：2015-01-01 00:00:00

  • Corrigendum to "Bioinformatics Analysis Reveals the Altered Gene Expression of Patients with Postmenopausal Osteoporosis Using Liuweidihuang Pills Treatment".

    abstract：:[This corrects the article DOI: 10.1155/2019/1907906.]. ...

    journal_title：BioMed research international

    pub_type： 杂志文章,已发布勘误

    doi：10.1155/2019/6897187

    authors： Gong R,Ren S,Chen M,Wang Y,Zhang G,Shi L,Zhang C,Su R,Li Y

    更新日期：2019-11-20 00:00:00

  • Comparison of Clinical Outcomes of Two-Level PELD and Foraminoplasty PELD for Highly Migrated Disc Herniations: A Comparative Study.

    abstract：Objective:The aim of this study is to compare the clinical outcomes of two-level percutaneous endoscopic lumbar discectomy (PELD) and foraminoplasty PELD in treating highly migrated lumbar disc herniations. Methods:Patients with highly migrated lumbar disc herniations were enrolled from May 2014 to June 2016. Low back...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2019/9681424

    authors： Wu X,Fan G,He S,Gu X,Yang Y

    更新日期：2019-10-13 00:00:00

  • The CD40 rs1883832 Polymorphism Affects Sepsis Susceptibility and sCD40L Levels.

    abstract：:Sepsis is a severe and progressive disease characterized by systemic inflammatory response syndrome (SIRS). CD40 serves as a vital link between immune response and inflammation. This study was designed to investigate the potential association between a functional single-nucleotide polymorphism (SNP) of CD40 (rs1883832...

    journal_title：BioMed research international

    pub_type： 临床试验,杂志文章

    doi：10.1155/2018/7497314

    authors： Liu ZL,Hu J,Xiao XF,Peng Y,Zhao SP,Xiao XZ,Yang MS

    更新日期：2018-03-26 00:00:00

  • Angiogenesis in the placenta: the role of reactive oxygen species signaling.

    abstract：:Proper placental development and function are central to the health of both the mother and the fetus during pregnancy. A critical component of healthy placental function is the proper development of its vascular network. Poor vascularization of the placenta can lead to fetal growth restriction, preeclampsia, and in so...

    journal_title：BioMed research international

    pub_type： 杂志文章,评审

    doi：10.1155/2015/814543

    authors： Pereira RD,De Long NE,Wang RC,Yazdi FT,Holloway AC,Raha S

    更新日期：2015-01-01 00:00:00

  • Transforaminal Percutaneous Endoscopic Lumbar Decompression by Using Rigid Bendable Burr for Lumbar Lateral Recess Stenosis: Technique and Clinical Outcome.

    abstract：Background:Open laminectomy has been regarded as the standard surgical procedure for lumbar lateral recess stenosis during the last decades. Although percutaneous endoscopic lumbar decompression has led to successful results comparable with open decompression, its application in LSS with is still challenging and techni...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2018/2601232

    authors： Tang S,Jin S,Liao X,Huang K,Luo J,Zhu T

    更新日期：2018-11-26 00:00:00

  • Age and Sex Effects on the Active Stiffness of Vastus Intermedius under Isometric Contraction.

    abstract：:Previously, a novel technique was proposed to quantify the relationship between the muscle stiffness and its nonfatigue contraction intensity. The method extended the measured range of isometric contraction to 100% maximum voluntary contraction (MVC) using an ultrasonic shear wave measurement setup. Yet, it has not be...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2017/9469548

    authors： Wang CZ,Guo JY,Li TJ,Zhou Y,Shi W,Zheng YP

    更新日期：2017-01-01 00:00:00

  • Specific growth rate determines the sensitivity of Escherichia coli to lactic acid stress: implications for predictive microbiology.

    abstract：:This study tested the hypothesis that sensitivity of Escherichia coli to lactic acid at concentrations relevant for fermented sausages (pH 4.6, 150 mM lactic acid, aw = 0.92, temperature = 20 or 27°C) increases with increasing growth rate. For E. coli strain 683 cultured in TSB in chemostat or batch, subsequent inacti...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2014/471317

    authors： Lindqvist R,Barmark G

    更新日期：2014-01-01 00:00:00

  • Evaluation of Antibiotic Resistance Pattern in Dental Bacteremia Detected by Multiplex PCR Technique.

    abstract：:The aim of this study was to detect oral bacteremia and offer the antibiotic resistance patterns. Bacterial resistance pattern was evaluated in 50 patients. A spectrophotometer device equipped with UV and electrophoresis of the extracted samples on agarose gel for antibiogram test were used. PCR test 15 minutes after ...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2020/9502959

    authors： Rezazadeh F,Azad A,Khorami A,Modaresi F,Rezaie Z

    更新日期：2020-10-01 00:00:00

  • Cubic and hexagonal liquid crystals as drug delivery systems.

    abstract：:Lipids have been widely used as main constituents in various drug delivery systems, such as liposomes, solid lipid nanoparticles, nanostructured lipid carriers, and lipid-based lyotropic liquid crystals. Among them, lipid-based lyotropic liquid crystals have highly ordered, thermodynamically stable internal nanostruct...

    journal_title：BioMed research international

    pub_type： 杂志文章,评审

    doi：10.1155/2014/815981

    authors： Chen Y,Ma P,Gui S

    更新日期：2014-01-01 00:00:00

  • The role of oxidative stress and inflammation in cardiovascular aging.

    abstract：:Age is an independent risk factor of cardiovascular disease, even in the absence of other traditional factors. Emerging evidence in experimental animal and human models has emphasized a central role for two main mechanisms of age-related cardiovascular disease: oxidative stress and inflammation. Excess reactive oxygen...

    journal_title：BioMed research international

    pub_type： 杂志文章,评审

    doi：10.1155/2014/615312

    authors： Wu J,Xia S,Kalionis B,Wan W,Sun T

    更新日期：2014-01-01 00:00:00

  • Effect of Chronic Kidney Disease on Changes in Vasopressin System Expression in the Kidney Cortex in Rats with Nephrectomy.

    abstract：:It is believed that the vasopressinergic system plays an important role in the pathogenesis of chronic kidney disease (CKD). The aim of this study was to evaluate the effect of CKD on changes in vasopressin system expression in the kidney cortex in rats with nephrectomy. The study was performed on 4 groups of Sprague ...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2018/2607928

    authors： Czarzasta K,Cudnoch-Jedrzejewska A,Niemczyk L,Wrzesien R,Tkaczyk M,Puchalska L,Saracyn M,Zmudzki W,Niemczyk S

    更新日期：2018-06-14 00:00:00

  • Interfractional variations of tumor centroid position and tumor regression during stereotactic body radiotherapy for lung tumor.

    abstract：PURPOSE:To determine interfractional changes of lung tumor centroid position and tumor regression during stereotactic body radiation therapy (SBRT). METHODS AND MATERIALS:34 patients were treated by SBRT in 4-5 fractions to a median dose of 50 Gy. The CT scans acquired for verification were registered with simulation ...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2014/372738

    authors： Sun Y,Lu Y,Cheng S,Guo W,Ye K,Zhao H,Zheng X,Li D,Wang S,Yang C,Ge H

    更新日期：2014-01-01 00:00:00

  • Burnout Is Associated with Reduced Parasympathetic Activity and Reduced HPA Axis Responsiveness, Predominantly in Males.

    abstract：:There is mounting evidence that burnout is a risk factor for cardiovascular disease (CVD). Stress-related dysregulation of the sympathetic and parasympathetic system and the hypothalamic pituitary adrenal (HPA) axis may explain the enhanced risk for CVD. To test this hypothesis, 55 patients (34 males and 21 females) w...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2015/431725

    authors： de Vente W,van Amsterdam JG,Olff M,Kamphuis JH,Emmelkamp PM

    更新日期：2015-01-01 00:00:00

  • The 3D Tele Motion Tracking for the Orthodontic Facial Analysis.

    abstract：:Aim. This study aimed to evaluate the reliability of 3D-TMT, previously used only for dynamic testing, in a static cephalometric evaluation. Material and Method. A group of 40 patients (20 males and 20 females; mean age 14.2 ± 1.2 years; 12-18 years old) was included in the study. The measurements obtained by the 3D-T...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2016/4932136

    authors： Mummolo S,Nota A,Marchetti E,Padricelli G,Marzo G

    更新日期：2016-01-01 00:00:00

  • Association between Triglyceride-Glucose Index and Type 2 Diabetes Mellitus in the Japanese Population: A Secondary Analysis of a Retrospective Cohort Study.

    abstract：:Triglyceride-glucose index (TyG index) is associated with type 2 diabetes mellitus (T2DM), but research on this relationship is limited in Japan. The purpose of this study was to evaluate the correlation between TyG index and the risk of T2DM in the Japanese population. Here, 12732 participants were selected from the ...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2020/2947067

    authors： Liu EQ,Weng YP,Zhou AM,Zeng CL

    更新日期：2020-12-11 00:00:00

  • Quality and Brands of Amoxicillin Formulations in Nairobi, Kenya.

    abstract：:Antibiotics are among the most counterfeited anti-infectious medicines in developing countries. Amoxicillin is one of the commonly prescribed, affordable, and easily accessible antibiotic in Kenya. It is a broad-spectrum antibiotic hence commonly used in chemotherapy. This study sought to determine the quality and ide...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2020/7091278

    authors： Koech LC,Irungu BN,Ng'ang'a MM,Ondicho JM,Keter LK

    更新日期：2020-06-12 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

  • Oxidative Stress Induced by Polymyxin E Is Involved in Rapid Killing of Paenibacillus polymyxa.

    abstract：:Historically, the colistin has been thought to kill bacteria through membrane lysis. Here, we present an alternative mechanism that colistin induces rapid Paenibacillus polymyxa death through reactive oxygen species production. This significantly augments our understanding of the mechanism of colistin action, which is...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2017/5437139

    authors： Yu Z,Zhu Y,Qin W,Yin J,Qiu J

    更新日期：2017-01-01 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

  • Acinetobacter baumannii Infection in Transfusion Dependent Thalassemia Patients with Sepsis.

    abstract：PURPOSE:To identify the Acinetobacter baumannii infection among transfusion dependent thalassemia patients. METHODS:A quantitative approach was employed to assess Acinetobacter baumannii infection in transfusion dependent thalassemia patients. Samples were collected from 916 patients, which have shown bacterial growth...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2017/2351037

    authors： Abdul Rasheed M,Alzahrani FM,Sattar Shaikh S

    更新日期：2017-01-01 00:00:00

  • Analysis of Transcription Factor-Related Regulatory Networks Based on Bioinformatics Analysis and Validation in Hepatocellular Carcinoma.

    abstract：:Hepatocellular carcinoma (HCC) accounts for a significant proportion of liver cancer, which has become the second most common cause of cancer-related mortality worldwide. To investigate the potential mechanisms of invasion and progression of HCC, bioinformatics analysis and validation by qRT-PCR were performed. We fou...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2018/1431396

    authors： Liu S,Yao X,Zhang D,Sheng J,Wen X,Wang Q,Chen G,Li Z,Du Z,Zhang X

    更新日期：2018-08-29 00:00:00

  • Phylogeography of Pteronotropis signipinnis, P. euryzonus, and the P. hypselopterus Complex (Teleostei: Cypriniformes), with Comments on Diversity and History of the Gulf and Atlantic Coastal Streams.

    abstract：:The cyprinid genus Pteronotropis is endemic to southeastern Gulf of Mexico and Atlantic Ocean of North America. Never before has the genus been demonstrated to be monophyletic. We investigate both the phylogenetic relationships and the phylogeography of some species in the genus using mitochondrial ND2 sequences. In n...

    journal_title：BioMed research international

    pub_type： 杂志文章

    doi：10.1155/2015/675260

    authors： Mayden RL,Allen J

    更新日期：2015-01-01 00:00:00

  • MicroRNAs and cardiovascular diseases.

    abstract：:Coronary artery diseases (CAD) and heart failure have high mortality rate in the world, although much progress has been made in this field in last two decades. There is still a clinical need for a novel diagnostic approach and a therapeutic strategy to decrease the incidence of CAD. MicroRNAs (miRNAs) are highly conse...

    journal_title：BioMed research international

    pub_type： 杂志文章,评审

    doi：10.1155/2015/682857

    authors： Nishiguchi T,Imanishi T,Akasaka T

    更新日期：2015-01-01 00:00:00