当前位置： SCI文献检索 > COMPUTATIONAL BIOLOGY AND CHEMISTRY期刊下所有文献 > Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO.

Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO.

Abstract：

:Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the protein Polyphenoloxidase (PPO). The protein was isolated from Mucuna pruriens and confirmed as tyrosinases involved in L-DOPA production. The activity was measured using different inhibitors at different concentrations taking catechol as substrate. A high-throughput binding study was conducted to compare the binding orientations of individual ligands and multiple ligands employing Autodock 4.2. The results of single substrate docking showed a better binding of urea with the binding energy of -3.48 kJ mol(-1) and inter molecular energy of -3.48 kJ mol(-1) while the results of MLSD revealed that ascorbic acid combined with the substrate showed better inhibition with a decreased binding energy of -2.37 kJ mol(-1).

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Raghavendra S,Aditya Rao SJ,Kumar V,Ramesh CK

doi

10.1016/j.compbiolchem.2015.09.008

subject

Has Abstract

pub_date

2015-12-01 00:00:00

pages

81-6

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(15)30170-5

journal_volume

59 Pt A

pub_type

杂志文章

相关文献

COMPUTATIONAL BIOLOGY AND CHEMISTRY文献大全
  • Conformational difference between two subunits in flavin mononucleotide binding protein dimers from Desulfovibrio vulgaris (MF): molecular dynamics simulation.

    abstract：:The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, su...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.05.007

    authors： Nunthaboot N,Lugsanangarm K,Pianwanit S,Kokpol S,Tanaka F,Nakanishi T,Kitamura M

    更新日期：2016-10-01 00:00:00

  • C3: An R package for cross-species compendium-based cell-type identification.

    abstract：:Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples becau...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.10.003

    authors： Kabir MH,Djordjevic D,O'Connor MD,Ho JWK

    更新日期：2018-12-01 00:00:00

  • Natural compounds as potential Hsp90 inhibitors for breast cancer-Pharmacophore guided molecular modelling studies.

    abstract：:Breast cancer is one of the major impediments affecting women globally. The ATP-dependant heat shock protein 90 (Hsp90) forms the central component of molecular chaperone machinery that predominantly governs the folding of newly synthesized peptides and their conformational maturation. It regulates the stability and f...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107113

    authors： Rampogu S,Parate S,Parameswaran S,Park C,Baek A,Son M,Park Y,Park SJ,Lee KW

    更新日期：2019-12-01 00:00:00

  • Dynamics of p53 and Wnt cross talk.

    abstract：:We present the mechanism of interaction of Wnt network module, which is responsible for periodic somitogenesis, with p53 regulatory network, which is one of the main regulators of various cellular functions, and switching of various oscillating states by investigating p53-Wnt model. The variation in Nutlin concentrati...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2015.07.014

    authors： Zubbair Malik M,Ali S,Alam MJ,Ishrat R,Brojen Singh RK

    更新日期：2015-12-01 00:00:00

  • Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation.

    abstract：:The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. The...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107241

    authors： Jin Z,Wang Y,Yu XF,Tan QQ,Liang SS,Li T,Zhang H,Shaw PC,Wang J,Hu C

    更新日期：2020-04-01 00:00:00

  • Drug-target interaction prediction by integrating multiview network data.

    abstract：:Drug-target interaction (DTI) prediction is a challenging step in further drug repositioning, drug discovery and drug design. The advent of high-throughput technologies brings convenience to the development of DTI prediction methods. With the generation of a high number of data sets, many mathematical models and compu...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2017.03.011

    authors： Zhang X,Li L,Ng MK,Zhang S

    更新日期：2017-08-01 00:00:00

  • Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction".

    abstract：:With advances in genomics, transcriptomics, metabolomics and proteomics, and more expansive electronic clinical record monitoring, as well as advances in computation, we have entered the Big Data era in biomedical research. Data gathering is growing rapidly while only a small fraction of this data is converted to usef...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章,评审

    doi：10.1016/j.compbiolchem.2015.08.005

    authors： Rouillard AD,Wang Z,Ma'ayan A

    更新日期：2015-12-01 00:00:00

  • The effect of structure on improvement of the PNA Young modulus: A study of steered molecular dynamics.

    abstract：:Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accord...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107133

    authors： Ghasemi RH,Keramati M,Mojarrad MHS

    更新日期：2019-12-01 00:00:00

  • Profiling of molecular pathways regulated by microRNA 601.

    abstract：:MicroRNAs (miRNAs) have been implicated in complex vertebrate developmental and pathological systems as a versatile class of molecules involved in the regulation of various biological processes and molecular pathways. To elucidate the role of miRNAs in human somatic cells, an understanding of the molecular framework r...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2009.09.003

    authors： Ohdaira H,Nakagawa H,Yoshida K

    更新日期：2009-12-01 00:00:00

  • Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies.

    abstract：:Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structu...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.05.004

    authors： Uba AI,Yelekçi K

    更新日期：2018-08-01 00:00:00

  • Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study.

    abstract：:Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Recept...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.02.019

    authors： Ozbek P

    更新日期：2016-06-01 00:00:00

  • Computer evaluation of VirE2 protein complexes for ssDNA transfer ability.

    abstract：:The single-stranded transfer DNA from the Ti plasmid of the soil bacteria Agrobacterium nonspecifically integrates into the plant chromosome and is inherited at subsequent cell divisions. How it is transferred across host membranes is unknown, but it is believed that VirE2 proteins form a membrane-spanning pore or cha...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2017.01.016

    authors： Volokhina I,Gusev Y,Mazilov S,Moiseeva Y,Chumakov M

    更新日期：2017-06-01 00:00:00

  • GeneMCL in microarray analysis.

    abstract：:Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edg...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2005.07.002

    authors： Samuel Lattimore B,van Dongen S,Crabbe MJ

    更新日期：2005-10-01 00:00:00

  • Chromatographic and computational screening of anisotropic lipophilicity and pharmacokinetics of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimides.

    abstract：:The present study is focused on a series of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimide derivatives, as potential anticonvulsants. The retention behavior of eleven succinimide derivatives was determined by using reversed phase high performance liquid chromatography (RP-HPLC) and reversed phase high performanc...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107161

    authors： Kovačević S,Banjac MK,Podunavac-Kuzmanović S,Milošević N,Ćurčić J,Vulić J,Šeregelj V,Banjac N,Ušćumlić G

    更新日期：2020-02-01 00:00:00

  • Mutually exclusive binding of APPL(PH) to BAR domain and Reptin regulates β-catenin dependent transcriptional events.

    abstract：:Reptin functions in a wide range of biological processes including chromatin remodelling, nucleolar organization and transcriptional regulation of WNT signalling. As β-catenin dependent transcriptional repression and activation events involve binding of Reptin and histone deacetylase 1 to APPL endocytic proteins, this...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2013.05.005

    authors： Rashid S,Parveen Z,Ferdous S,Bibi N

    更新日期：2013-12-01 00:00:00

  • Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization.

    abstract：:Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SN...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2008.07.029

    authors： Chang HW,Yang CH,Ho CH,Wen CH,Chuang LY

    更新日期：2009-02-01 00:00:00

  • A novel k-word relative measure for sequence comparison.

    abstract：:In order to extract phylogenetic information from DNA sequences, the new normalized k-word average relative distance is proposed in this paper. The proposed measure was tested by discriminate analysis and phylogenetic analysis. The phylogenetic trees based on the Manhattan distance measure are reconstructed with k ran...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.10.007

    authors： Tang J,Hua K,Chen M,Zhang R,Xie X

    更新日期：2014-12-01 00:00:00

  • Circular code motifs in the ribosome decoding center.

    abstract：:A translation (framing) code based on the circular code was proposed in Michel (2012) with the identification of X circular code motifs (X motifs shortly) in the bacterial rRNA of Thermus thermophilus, in particular in the ribosome decoding center. Three classes of X motifs are now identified in the rRNAs of bacteria ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.08.001

    authors： El Soufi K,Michel CJ

    更新日期：2014-10-01 00:00:00

  • Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin.

    abstract：:Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from ri...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107245

    authors： Hussain A,Shahbaz M,Tariq M,Ibrahim M,Hong X,Naeem F,Khalid Z,Raza HMZ,Bo Z,Bin L

    更新日期：2020-06-01 00:00:00

  • Determining common insertion sites based on retroviral insertion distribution across tumors.

    abstract：:A CIS (common insertion site) indicates a genome region that is hit more frequently by retroviral insertions than expected by chance. Such a region is strongly related to cancer gene loci, which leads to the detection of cancer genes. An algorithm for detecting CISs should satisfy the following: (1) it does not requir...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.03.001

    authors： Chen F,Li Z,Chen YP

    更新日期：2014-08-01 00:00:00

  • Predicting human intestinal absorption of diverse chemicals using ensemble learning based QSAR modeling approaches.

    abstract：:Human intestinal absorption (HIA) of the drugs administered through the oral route constitutes an important criterion for the candidate molecules. The computational approach for predicting the HIA of molecules may potentiate the screening of new drugs. In this study, ensemble learning (EL) based qualitative and quanti...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.01.005

    authors： Basant N,Gupta S,Singh KP

    更新日期：2016-04-01 00:00:00

  • Putative dual inhibitors of Janus kinase 1 and 3 (JAK1/3): Pharmacophore based hierarchical virtual screening.

    abstract：:Janus kinase 1 and 3 are non-receptor protein tyrosine kinases, involved in the regulation of various cytokines implicated in the pathogenesis of autoimmune and inflammatory disease conditions. Thus, they serve as therapeutic targets for the designing of multi-targeted agents for the treatment of inflammatory-mediated...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.07.009

    authors： Jasuja H,Chadha N,Singh PK,Kaur M,Bahia MS,Silakari O

    更新日期：2018-10-01 00:00:00

  • The complex task of choosing a de novo assembly: lessons from fungal genomes.

    abstract：:Selecting the values of parameters used by de novo genomic assembly programs, or choosing an optimal de novo assembly from several runs obtained with different parameters or programs, are tasks that can require complex decision-making. A key parameter that must be supplied to typical next generation sequencing (NGS) a...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.08.014

    authors： Gallo JE,Muñoz JF,Misas E,McEwen JG,Clay OK

    更新日期：2014-12-01 00:00:00

  • A vibrational entropy term for DNA docking with autodock.

    abstract：:DNA interacts with small molecules, from water to endogenous reactive oxygen and nitrogen species, environmental mutagens and carcinogens, and pharmaceutical anticancer molecules. Understanding and predicting the physical interactions of small molecules with DNA via docking is key not only for the comprehension of mol...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.03.027

    authors： McElfresh GW,Deligkaris C

    更新日期：2018-06-01 00:00:00

  • MATEPRED-A-SVM-Based Prediction Method for Multidrug And Toxin Extrusion (MATE) Proteins.

    abstract：:The growth and spread of drug resistance in bacteria have been well established in both mankind and beasts and thus is a serious public health concern. Due to the increasing problem of drug resistance, control of infectious diseases like diarrhea, pneumonia etc. is becoming more difficult. Hence, it is crucial to unde...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2015.07.011

    authors： Tamanna,Ramana J

    更新日期：2015-10-01 00:00:00

  • Biochemical and computational insights of adenosine deaminase inhibition by Epigallocatechin gallate.

    abstract：:Epigallocatechin gallate, a flavonoid from Camellia sinensis possess various pharmacological activities such as anticancer, antimicrobial and antioxidant etc. Adenosine deaminase, (ADA), is a key enzyme involved in the purine metabolism, the inhibitors of which is being considered as highly promising candidate for the...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107111

    authors： K G A,C S S,J A,C S

    更新日期：2019-12-01 00:00:00

  • Genome-wide identification and expression analysis of SWI1 genes in Boechera species.

    abstract：:As a mode of reproduction in plants, apomixis leads to the generation of clones via seeds. Apomictic plants form viable diploid female gametes without meiosis (apomeiosis) and produce embryos without fertilization (parthenogenesis). Apomeiosis, as a major component of apomixis, has recently been reported in some Arabi...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.04.004

    authors： Sezer F,Yüzbaşioğlu G,Özbilen A,Taşkin KM

    更新日期：2016-06-01 00:00:00

  • Identification and characterization of lysine-methylated sites on histones and non-histone proteins.

    abstract：:Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.01.009

    authors： Lee TY,Chang CW,Lu CT,Cheng TH,Chang TH

    更新日期：2014-06-01 00:00:00

  • Computational analysis for the determination of deleterious nsSNPs in human MTHFR gene.

    abstract：:Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.02.022

    authors： Desai M,Chauhan JB

    更新日期：2018-06-01 00:00:00

  • Modelling the role of dual specificity phosphatases in herceptin resistant breast cancer cell lines.

    abstract：BACKGROUND:Breast cancer remains the most lethal type of cancer for women. A significant proportion of breast cancer cases are characterised by overexpression of the human epidermal growth factor receptor 2 protein (HER2). These cancers are commonly treated by Herceptin (Trastuzumab), but resistance to drug treatment f...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.03.018

    authors： Buiga P,Elson A,Tabernero L,Schwartz JM

    更新日期：2019-06-01 00:00:00