Protein Data Bank

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  • Prediction By Komputer Assisted Technology : Lab Analysis

    760 Words  | 4 Pages

    In the materials and methods section; ligand preparation, target protein identification and preparation, molecular descriptors calculation, ADME (Absorption, Distribution, Metabolism and Excretion) and TOPKAT (Toxicity Prediction by Komputer Assisted Technology) analysis were carried out according to the previously reported method as briefly stated below. Ligand preparation Chemical structures of the ligands i) asperyellone [CID101600052]; ii) asperenone [CID5368642]; iii) hydroasperyellone [CID561143];

  • Pdb Enzyme Lab

    596 Words  | 3 Pages

    structure of enzyme Plasmodium falciparum enzyme farnesyltransferase was not found available in Protein Data Bank (PDB) archive, therefore the structure was built using homology modeling method. In order to predict the structure of enzyme (PfFT), the sequence of enzyme IDs PF3D7_1242600 [alpha- subunit] and PF3D7_1147500 [beta subunit] were obtained from the web services (www.gene db.org), protein sequence data bank in swiss prot or uniprock KB (Q8IHP6), NCBI (AAW78025). The only sequence of the active site

  • Zinc Binds To Protein

    371 Words  | 2 Pages

    How does zinc binds to proteins? Zinc coordinates proteins with four different surroundings with different roles: catalytic, co-catalytic, structural and interface. In many proteins Zn2+ ions also serve to correct polypeptide folding. Furthermore, zinc is a cofactor in all six enzyme classes. Zinc ions in protein interface may influence the formation of stable quaternary structures, as in the case of hexameric insulin, which is formed from three protein dimers and two Zn2+ ions. As has been said

  • Neph Case Study

    1070 Words  | 5 Pages

    All four types ENRs require cofactors as an electron donor. FabI requires either of NADH or NADPH as cofactors.7 In the case of FabK, NADH is reductant, but acts indirectly by reducing the tightly bound Flavin cofactor.20 FabL uses NADPH as a cofactor,11 and FabV prefers NADH than NADPH.14 Therefore, we attempted to co-crystalize the vfFabV with its cofactor NADH. However, we were not able to succeed in observing interpretable electron density map for bound NADH. Until now, there are three available

  • Polyphen2.0 Synthesis

    299 Words  | 2 Pages

    characterizes the amino acid substitution (Ramensky et al. 2002). To determine the effect of variants on the protein secondary structure, inter chain contents, functional sites, and binding sites, Polyphen2.0 utilizes PDB (Protein Data Bank), DSSP (Dictionary of secondary structures in protein), and three-dimensional structure databases (Ramensky et al. 2002). We submitted the query in the form of the protein sequence with the mutational position of two amino

  • Ea-OTU ) Case Study

    1079 Words  | 5 Pages

    acervulina remains unclear. Protein ubiquitination regulates cellular processes by influencing the stability and function of modified proteins. The ubiquitin (Ub) protein is highly conserved in all eukaryotes and composed of 76 amino acids. A single Ub protein or Ub oligomers can modify single or multiple lysine residues of the protein. Ubiquitin forms covalent chains through each of its seven lysine residues (Lys6, Lys11, Lys27,

  • Cell Proliferation And The Control Of Cellular Function

    1228 Words  | 5 Pages

    erythrocytes (Homer et al., 2000). The 70 kDa heat-shock proteins (HSP-70s) are intracellular proteins found in all organisms. HSPs play important roles in cell proliferation and the control of cellular functions (Lindquist, 1986). Heat shock proteins (HSPs) are known as stress proteins because various forms of stress enhance their transcriptional activation and biosynthesis (Lindquist, 1986). As many bacteria and parasites produce HSP-70, the protein serves as an antigen for bacteria and parasitic pathogens

  • How The Cells Are The Way Of Life?

    823 Words  | 4 Pages

    making up proteins-the nucleus, ribosomes, rough ER, and the golgi apparatus (Alberts, B. 2014). Proteins are very critical to cells, because they happen to be assembled by proteins, which in turn becomes major jobs that it does for

  • In this study, 1) an explanation on the derivation of the knowledge based PMF for pairwise

    700 Words  | 3 Pages

    3D structure prediction will be suggested. 1) The search for methods for protein structure prediction has been a matter of study for the last 60 years [1]. In 1990, Sippl [2] proposed a method that could be applied to protein structure prediction using “potentials of mean force” (PMF) based on information from known protein conformation (available at the Protein Data Bank). Creating a tertiary structure model of a protein with unknown structure is the

  • The Earth 's Oceans And Its Impact On Earth

    1269 Words  | 6 Pages

    fisheries will completely collapse by 2048 (Barkin page 1). While these are just facts that tell the worst-case scenario, they should be alarms that spark change in the way we fish. This paper, however, will specifically target overfishing in the Grand Banks in Newfoundland, Canada, and analyze its impact on Earth, its Environment and Humanity. Over fishing is simply when fishermen catch more fish than are being reproduced. Eventually the stock of fish in the environment will be completely depleted. That

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