当前位置： SCI文献检索 > COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING期刊下所有文献 > Protein Sequence Comparison and DNA-binding Protein Identification with Generalized PseAAC and Graphical Representation.

Protein Sequence Comparison and DNA-binding Protein Identification with Generalized PseAAC and Graphical Representation.

Abstract：

AIM AND OBJECTIVE:The rapid increase in the amount of protein sequence data available leads to an urgent need for novel computational algorithms to analyze and compare these sequences. This study is undertaken to develop an efficient computational approach for timely encoding protein sequences and extracting the hidden information. METHODS:Based on two physicochemical properties of amino acids, a protein primary sequence was converted into a three-letter sequence, and then a graph without loops and multiple edges and its geometric line adjacency matrix were obtained. A generalized PseAAC (pseudo amino acid composition) model was thus constructed to characterize a protein sequence numerically. RESULTS:By using the proposed mathematical descriptor of a protein sequence, similarity comparisons among β-globin proteins of 17 species and 72 spike proteins of coronaviruses were made, respectively. The resulting clusters agreed well with the established taxonomic groups. In addition, a generalized PseAAC based SVM (support vector machine) model was developed to identify DNA-binding proteins. Experiment results showed that our method performed better than DNAbinder, DNA-Prot, iDNA-Prot and enDNA-Prot by 3.29-10.44% in terms of ACC, 0.056-0.206 in terms of MCC, and 1.45-15.76% in terms of F1M. When the benchmark dataset was expanded with negative samples, the presented approach outperformed the four previous methods with improvement in the range of 2.49-19.12% in terms of ACC, 0.05-0.32 in terms of MCC, and 3.82- 33.85% in terms of F1M. CONCLUSION:These results suggested that the generalized PseAAC model was very efficient for comparison and analysis of protein sequences, and very competitive in identifying DNA-binding proteins.

journal_name

Comb Chem High Throughput Screen

journal_title

Combinatorial chemistry & high throughput screening

authors

Li C,Zhao J,Wang C,Yao Y

doi

10.2174/1386207321666180130100838

subject

Has Abstract

pub_date

2018-01-01 00:00:00

pages

100-110

issue

2

eissn

1386-2073

issn

1875-5402

pii

CCHTS-EPUB-88267

journal_volume

21

pub_type

杂志文章

相关文献

COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING文献大全
  • DABCO Catalyzed Green and Efficient Synthesis of 2-Amino-4H-Pyrans and Their Biological Evaluation as Antimicrobial and Anticancer Agents.

    abstract：AIM AND OBJECTIVE:The present method is simple, green and highly efficient for the synthesis of 2-amino-4H-pyran derivatives which are achieved by a one pot three component cyclocondensation of aldehyde, malanonitrile and ethyl acetoacetate or methyl acetoacetate using DABCO under solvent free with grinding conditions ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207321666180315095422

    authors： Waghmare AS,Pandit SS,Suryawanshi DM

    更新日期：2018-01-01 00:00:00

  • Correlative Study of Bone-Related Biochemicals and Endocrine Changes in Perimenopausal Women in Enugu, Nigeria.

    abstract：BACKGROUND AND OBJECTIVE:Perimenopause is a physiological occurrence in women, and is characterized by endocrine and biochemical changes. During perimenopause phase, many derangements or abnormal health conditions start developing as a result of hormonal changes. These derangements in health conditions and biochemical ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207323666201023120212

    authors： Ikegwuonu CI,Uchendu IK,Maduka CI

    更新日期：2020-10-23 00:00:00

  • Scutellaria barbata flavonoids improve the composited Aβ-induced abnormal changes of glial cells in rats' brain.

    abstract：AIM:It has been reported that glial cells are involved in Alzheimer's disease (AD). According to our previous research, Scutellaria barbata flavonoids (SBFs) can protect the neuronal disorder and memory impairment for AD-like rats, while the effect of SBFs on the glial cells disorder in AD-like rats has been less well ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207323666201209092358

    authors： Cheng JJ,Guo Q,Wu XG,Ma S,Gao Y,Ya-Zhen S

    更新日期：2020-12-08 00:00:00

  • Structural Exploration of Synthetic Chromones as Selective MAO-B Inhibitors: A Mini Review.

    abstract：AIM AND OBJECTIVE:Specific inhibitors of monoamine oxidase (MAO)-B are considered useful therapeutic agents in targeting neurological disorders like Alzheimer's and Parkinson's diseases. Due to the academic challenge of designing new hMAO-B inhibitors and the possibility of discovering compounds with improved propertie...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/1386207320666170227155517

    authors： Mathew B,Mathew GE,Petzer JP,Petzer A

    更新日期：2017-01-01 00:00:00

  • Thermodynamics of molecular recognition of bile salts by 3,6'-(oligoethylenediamino-bridged) beta-cyclodextrin dimers.

    abstract：:The molecular recognition behaviors of some representative bile salts by three 3,6'-bridged beta-cyclodextrin dimers with oligo(ethylenediamino) linkers in different lengths, i.e. 3,6'-(ethylenediamino-bridged) beta-cyclodextrin dimer (1), 3,6'-(diethylenetriamino-bridged) beta-cyclodextrin dimer (2), and 3,6'-(trieth...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/138620707781662844

    authors： Liu Y,Kang S,Chen Y,Cao R,Shi J

    更新日期：2007-06-01 00:00:00

  • Resisting the Resistance in Cancer: Cheminformatics Studies on Short- Path Base Excision Repair Pathway Antagonists Using Supervised Learning Approaches.

    abstract：:Survival of cells and maintenance of genome depend on detection and repair of damaged DNA through intricate mechanisms. Cancer treatment relies on chemotherapy or radiation therapy that kills neoplastic cells by causing immense damage to the DNA. In many cases, escalated DNA repair mechanism leads to resistance agains...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207318666150626093648

    authors： Jain R,Jamal S,Goyal S,Wahi D,Singh A,Grover A

    更新日期：2015-01-01 00:00:00

  • Synthesis of 1,4,5-trisubstituted 1,2,3-triazoles amicable for automation.

    abstract：:A three-component 3+2 cycloaddition reaction followed by Suzuki coupling reaction was carried out to synthesize a library of compounds using automation (parallel synthesizer). Scaffolds that are unexplored in literature were used for the synthesis of library. The iodo-triazoles formed by 3+2 cycloaddition reaction wer...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207311316080009

    authors： Kavitha M,Mahipal B,Mainkar PS,Chandrasekhar S

    更新日期：2013-09-01 00:00:00

  • Moving pictures: imaging flow cytometry for drug development.

    abstract：:As technologies for high throughput and high content screening continue to evolve, new platforms for quantitative cellular imaging will play an increasingly important role in identifying and profiling lead compounds. To gain insight into the effects of a compound on cell morphology or intracellular events, it is neces...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/138620709789383204

    authors： Elliott GS

    更新日期：2009-11-01 00:00:00

  • Ligand-based pharmacophore modeling, atom-based 3D-QSAR and molecular docking studies on substituted thiazoles and thiophenes as polo-like kinase 1 (Plk1) inhibitors.

    abstract：:Polo-like kinase 1 (Plk1) is a decisive enzyme with its multifunctional activity in cell cycle progression especially mitosis. The over expression of Plk1 in broad spectrum of cancer types turns into a promising therapeutic target against cancer. In the present study, several ligand based pharmacophore models and atom...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207317666141024152910

    authors： Chekkara R,Gorla VR,Susithra E,Tenkayala SR

    更新日期：2014-01-01 00:00:00

  • Exploration of the Potential Mechanism of Calculus Bovis in Treatment of Primary Liver Cancer by Network Pharmacology.

    abstract：AIM AND OBJECTIVE:Calculus Bovis (CB) has been employed to treat diseases for a long time. It has been identified to play significant anti-inflammatory and anti-tumor roles. However, the mechanism of treating primary liver cancer (PLC) remains to be revealed. This study aims to clarify the molecules and mechanisms of C...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207323666200808172051

    authors： Zhang Z,Zeng P,Gao W,Wu R,Deng T,Chen S,Tian X

    更新日期：2021-01-01 00:00:00

  • Expression Levels of A Disintegrin-like Metalloproteinase with Thrombospondin Motifs-4 and -5 (ADAMTS-4 and ADAMTS-5) in Inflamed and Healthy Gingival Tissues.

    abstract：BACKGROUND:ADAMTS (A disintegrin-like metalloproteinase with thrombospondin motifs) is a group of 19 zinc-dependent metalloproteases known to function in many pathological and physiological processes, such as adhesion, cell fusion, signaling, proteolysis and ECM degradation. OBJECTIVES:The aim of this study was to dem...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207323666200218113000

    authors： Tayman MA,Koyuncu İ,Köklü NÖ

    更新日期：2020-01-01 00:00:00

  • Massively parallel screening of the receptorome.

    abstract：:The National Institute of Mental Health (NIMH) Psychoactive Drug Screening Program (PDSP) is a resource that provides free screening of novel compounds to academic investigators. This program differs from other public-sector screening programs in that compounds are screened against a large panel of transmembrane recep...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/138620708784911483

    authors： Jensen NH,Roth BL

    更新日期：2008-07-01 00:00:00

  • Cascade synthesis with (triphenylphosphoranylidene)-ethenone as a versatile reagent for fast synthesis of heterocycles and unsaturated amides under microwave dielectric heating.

    abstract：:A general procedure for the synthesis of a large variety of compounds comprising an alpha, beta,-unsaturated carbonyl functionality was developed. The use of one-pot cascade synthesis with (triphenylphosphora-nylidene)ethenone as a versatile reagent for various formations including heterocycles of different ring sizes...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207023330066

    authors： Westmana J,Orrling K

    更新日期：2002-11-01 00:00:00

  • Inhibition of P-Glycoprotein Mediated Efflux of Paclitaxel by Coumarin Derivatives in Cancer Stem Cells: An In Silico Approach.

    abstract：:P-glycoprotein (P-gp) is well known to cause multidrug resistance (MDR) in cancer cells. This MDR leads to cancer recurrence which is a major obstacle in cancer treatment. High P-gp expression has been observed in the population of cancer stem cells (CSCs) having self-renewal potential. Early detection and inhibition ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 历史文章,杂志文章

    doi：10.2174/1386207319666160517115158

    authors： Tripathi A,Misra K

    更新日期：2016-01-01 00:00:00

  • Recent developments of in silico predictions of oral bioavailability.

    abstract：:Unfavorable oral bioavailability is an important reason accounting for the failure of the drug candidates. Considering the lack of in vitro high-throughput screening assay for oral bioavailability, it is critical to develop in silico models for early predictions of oral bioavailability. In this review, we summarize pr...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/138620711795508368

    authors： Zhu J,Wang J,Yu H,Li Y,Hou T

    更新日期：2011-06-01 00:00:00

  • New Research for Quinazoline-2,4-diones as HPPD Inhibitors Based on 2D-MLR and 3D-QSAR Models.

    abstract：AIM AND OBJECTIVE:4-Hydroxyphenylpyruvate dioxygenase (HPPD), converting phydroxyphenylpyruvate (HPPA) to homogentisate (HGA), is an important target for treating type I tyrosinemia and synthesizing novel herbicides due to its significant role in tyrosine catabolism. Hence, it is imperative to design novel HPPD inhibit...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207320666170622073738

    authors： Fu Y,Sun YN,Cao HF,Yi KH,Zhao LX,Li JZ,Ye F

    更新日期：2017-01-01 00:00:00

  • Growth hormone secretagogues.

    abstract：:Growth hormone secretagogues (GHSs) are synthetic molecules that stimulate and amplify pulsatile pituitary growth hormone release, via a separate pathway distinct from GH releasing hormone/somatostatin. The activity of GHSs is not fully specific for GH secretion; some GHSs also have slight releasing activity on other ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/138620706776055458

    authors： Isidro ML,Cordido F

    更新日期：2006-03-01 00:00:00

  • Combination therapy: the propitious rationale for drug development.

    abstract：:Therapeutic options for many infections are extremely limited and at crisis point. We run the risk of entering a second pre-antibiotic era. There had been no miracle drug for the patients infected by resistant microbial pathogens. Most of the very few new drugs under development have problems with their toxicity, or p...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/13862073113166660065

    authors： Phougat N,Khatri S,Singh A,Dangi M,Kumar M,Dabur R,Chhillar AK

    更新日期：2014-01-01 00:00:00

  • Structural Comparison of Gene Relevance Networks for Breast Cancer Tissues in Different Grades.

    abstract：BACKGROUND:The breast is an important biological system of human with two distinct states, i.e. normal and tumoral. Research on breast cancer could be based on systematic modeling to contrast the system structures of these two states. OBJECTIVE:We use mutual information for the construction of the gene network of brea...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207319666160831152801

    authors： Zhang Y,Dong Y,Lv K,Zhao Q,Su J

    更新日期：2016-01-01 00:00:00

  • Fluorous-enhanced multicomponent reactions for making drug-like library scaffolds.

    abstract：:Multicomponent reactions (MCRs) generate multiple bonds in a single reaction process, which is highly efficient to construct relatively complex molecules. Conducting post-MCR modification reactions further increases the molecular complexity and diversity. MCR has become a powerful approach to make drug-like molecules ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/138620707780126697

    authors： Zhang W

    更新日期：2007-03-01 00:00:00

  • Bioactivity-Guided Isolation of Antiproliferative Sesquiterpene Lactones from Centaurea solstitialis L. ssp. solstitialis.

    abstract：:Centaurea solstitialis L. ssp. solstitialis (CSS) has been used as medicine for various diseases. In this work, root, stem and flower parts of the plant were separately extracted with methanol to execute bioassay-guided isolation. Antiproliferative activities of each extracts on C6 cells (Rat Brain tumor cells) and He...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207319666151203002117

    authors： Erenler R,Sen O,Yaglioglu AS,Demirtas I

    更新日期：2016-01-01 00:00:00

  • Chemoinformatics Approach for Building Molecular Networks from Marine Organisms.

    abstract：:Natural products obtained from marine sources are considered to be a rich and diverse source of potential drugs. In the present work we demonstrate the use of chemoinformatics approach for the design of new molecules inspired by molecules from marine organisms. Accordingly we have assimilated information from two majo...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207318666150703112950

    authors： Karthikeyan M,Nimje D,Pahujani R,Tyagi K,Bapat S,Vyas R,Pillai Padmakumar K

    更新日期：2015-01-01 00:00:00

  • The use of polymer-bound triphenylphosphine in the stereochemical inversion of secondary alcohols.

    abstract：:Polymer-bound triphenylphosphine can replace triphenylphosphine in the Mitsunobu reaction to generate stereochemically inverted secondary alcohols. This method is comparable with the standard Mitsunobu reaction in terms of inversion of stereochemistry, yield, and reaction time, even for sterically very hindered second...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207003331706

    authors： White JM,Tunoori AR,Dutta D,Georg GI

    更新日期：2000-04-01 00:00:00

  • Structure-based modeling of dye-fiber affinity with SOM-4D-QSAR paradigm: application to set of anthraquinone derivatives.

    abstract：:A comparative structure-affinity study of anthraquinone dyes adsorption on cellulose fibre is presented in this paper. We used receptor-dependent 4D-QSAR methods based on grid and neural (SOM) methodology coupled with IVEPLS procedure. The applied RD 4D-QSAR approach focuses mainly on the ability of mapping dye proper...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207317666140205195252

    authors： Bak A,Wyszomirski M,Magdziarz T,Smolinski A,Polanski J

    更新日期：2014-01-01 00:00:00

  • The role of in vitro ADME assays in antimalarial drug discovery and development.

    abstract：:The high level of attrition of drugs in clinical development has led pharmaceutical companies to increase the efficiency of their lead identification and development through techniques such as combinatorial chemistry and high-throughput (HTP) screening. Since the major reasons for clinical drug candidate failure other...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/1386207053328129

    authors： Shearer TW,Smith KS,Diaz D,Asher C,Ramirez J

    更新日期：2005-02-01 00:00:00

  • Establishment of a secondary screening assay for P/Q-type calcium channel blockers.

    abstract：:Development of calcium channel blockers is attractive, but has in the past been hampered by lack of high throughput electrophysiological technology. This limitation has been overcome by the implementation of automated patch clamp systems that allow identification of state-dependent compounds, which preferentially targ...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207311316030008

    authors： Hermann D,Mezler M,Swensen AM,Bruehl C,Obergrußerger A,Wicke K,Schoemaker H,Gross G,Draguhn A,Nimmrich V

    更新日期：2013-03-01 00:00:00

  • Target identification strategies in chemical genetics.

    abstract：:Chemical inhibitors have had a profound impact on many diverse fields of biology. The goal of chemical genetics is to use small molecules to perturb biological systems in a manner conceptually similar to traditional genetics. Key to the advancement of the chemical genetic paradigm is the further development of tools a...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章,评审

    doi：10.2174/1386207043328391

    authors： Tochtrop GP,King RW

    更新日期：2004-11-01 00:00:00

  • High throughput screening and structure-activity relationship study of potential α2A-adrenoceptor agonists by LANCETM cAMP assay.

    abstract：:G protein-coupled receptors (GPCRs) are signaling molecules with a wide variety of skills. Members of this large family of membrane protein have been shown to regulate the activities of the different signaling pathways of the ligand specific manner. α2-adrenoceptors (α2-ARs) are one of the GPCRs and the stimulation of...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207311316070003

    authors： Yang H,He L,Yan M,He JG,Yu T

    更新日期：2013-06-28 00:00:00

  • Mechanistic Insights to the Binding of Antibody CR3022 Against RBD from SARS-CoV and HCoV-19/SARS-CoV-2: A Computational Study.

    abstract：Aims & Objective:Corona Virus Disease 2019 (COVID-19) caused by the human coronavirus 2019 (HCoV-19, also known as SARS-CoV-2) infection is currently in a global outbreak. COVID-19 has posed a huge threat to public health and economic stability worldwide. CR3022, a human monoclonal neutralizing antibody isolated from a...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207323666201026160500

    authors： Yu W,Wu X,Ren J,Zhang X,Wang Y,Li C,Xu W,Li J,Li G,Zheng W,Liao H,Yuan X

    更新日期：2020-10-26 00:00:00

  • Plasma-Free Amino Acid Profiling of Nasal Polyposis Patients.

    abstract：AIM AND OBJECTIVE:To determine the mechanisms present in the etiopathogenesis of nasal polyposis. It is not clear whether amino acids contribute in a causal way to the development of the disease. Therefore, the aim of this study was to determine the plasma-free amino acid profile in patients with nasal polyposis and to...

    journal_title：Combinatorial chemistry & high throughput screening

    pub_type： 杂志文章

    doi：10.2174/1386207322666190920110324

    authors： Celik M,Şen A,Koyuncu İ,Gönel A

    更新日期：2019-01-01 00:00:00