Aleksey Porollo

Summary

Affiliation: University of Cincinnati
Country: USA

Publications

  1. ncbi request reprint Large-scale characterization of introns in the Pneumocystis carinii genome
    Bradley E Slaven
    University of Cincinnati College of Medicine, Cincinnati, Ohio 46267 0560, USA
    J Eukaryot Microbiol 53:S151-3. 2006
  2. ncbi request reprint Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome
    Aleksey Porollo
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267 0056, USA
    Curr Drug Targets 13:1575-85. 2012
  3. pmc POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations
    Aleksey Porollo
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
    Nucleic Acids Res 38:W662-6. 2010
  4. pmc Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D
    Aleksey Porollo
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
    BMC Bioinformatics 8:316. 2007
  5. pmc Survey of public domain software for docking simulations and virtual screening
    Jacek Biesiada
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, OH 45229, USA
    Hum Genomics 5:497-505. 2011
  6. ncbi request reprint Draft assembly and annotation of the Pneumocystis carinii genome
    Bradley E Slaven
    University of Cincinnati College of Medicine, Cincinnati, Ohio 46267 0560, USA
    J Eukaryot Microbiol 53:S89-91. 2006
  7. doi request reprint Enhanced prediction of conformational flexibility and phosphorylation in proteins
    Karthikeyan Swaminathan
    Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
    Adv Exp Med Biol 680:307-19. 2010
  8. doi request reprint On setting up and assessing docking simulations for virtual screening
    Jacek Biesiada
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, OH, USA
    Methods Mol Biol 928:1-16. 2012
  9. pmc Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite
    Melanie T Cushion
    University of Cincinnati College of Medicine, Department of Internal Medicine, Division of Infectious Diseases, Cincinnati, Ohio, United States of America
    PLoS ONE 2:e423. 2007
  10. pmc CYP63A2, a catalytically versatile fungal P450 monooxygenase capable of oxidizing higher-molecular-weight polycyclic aromatic hydrocarbons, alkylphenols, and alkanes
    Khajamohiddin Syed
    Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
    Appl Environ Microbiol 79:2692-702. 2013

Collaborators

Detail Information

Publications18

  1. ncbi request reprint Large-scale characterization of introns in the Pneumocystis carinii genome
    Bradley E Slaven
    University of Cincinnati College of Medicine, Cincinnati, Ohio 46267 0560, USA
    J Eukaryot Microbiol 53:S151-3. 2006
  2. ncbi request reprint Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome
    Aleksey Porollo
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267 0056, USA
    Curr Drug Targets 13:1575-85. 2012
    ..A summary of genomic sequences within Pneumocystis carinii associated with the corresponding targeted biological pathways is provided. All sequences are available via the Pneumocystis Genome Project at http://pgp.cchmc.org/...
  3. pmc POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations
    Aleksey Porollo
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
    Nucleic Acids Res 38:W662-6. 2010
    ..URL: http://polyview.cchmc.org/conform.html...
  4. pmc Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D
    Aleksey Porollo
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
    BMC Bioinformatics 8:316. 2007
    ..These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs...
  5. pmc Survey of public domain software for docking simulations and virtual screening
    Jacek Biesiada
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, OH 45229, USA
    Hum Genomics 5:497-505. 2011
    ..The methods tested here yielded a correlation coefficient of up to 0.6 between the predicted and observed binding affinities for active compounds in this benchmark...
  6. ncbi request reprint Draft assembly and annotation of the Pneumocystis carinii genome
    Bradley E Slaven
    University of Cincinnati College of Medicine, Cincinnati, Ohio 46267 0560, USA
    J Eukaryot Microbiol 53:S89-91. 2006
  7. doi request reprint Enhanced prediction of conformational flexibility and phosphorylation in proteins
    Karthikeyan Swaminathan
    Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
    Adv Exp Med Biol 680:307-19. 2010
    ..In this study, we developed and compared one- and two-class support vector machine (SVM)-based predictors for several commonly used sets of attributes. [These predictors are being made available at http://sable.cchmc.org/]...
  8. doi request reprint On setting up and assessing docking simulations for virtual screening
    Jacek Biesiada
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, OH, USA
    Methods Mol Biol 928:1-16. 2012
    ..Here, we primarily focus on solutions for several public domain packages that are widely used in the context of drug development...
  9. pmc Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite
    Melanie T Cushion
    University of Cincinnati College of Medicine, Department of Internal Medicine, Division of Infectious Diseases, Cincinnati, Ohio, United States of America
    PLoS ONE 2:e423. 2007
    ..This study represents the first characterization of the expressed genes of a non-culturable fungal pathogen of mammals during the infective process...
  10. pmc CYP63A2, a catalytically versatile fungal P450 monooxygenase capable of oxidizing higher-molecular-weight polycyclic aromatic hydrocarbons, alkylphenols, and alkanes
    Khajamohiddin Syed
    Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
    Appl Environ Microbiol 79:2692-702. 2013
    ..g., crude oil spills)...
  11. ncbi request reprint Prediction-based fingerprints of protein-protein interactions
    Aleksey Porollo
    Division of Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, Ohio 45229, USA
    Proteins 66:630-45. 2007
    ..42, as opposed to up to 70% classification accuracy and up to 0.3 Matthews correlation coefficient for methods that do not utilize RSA prediction-based fingerprints. The new method is available at http://sppider.cchmc.org...
  12. pmc Rational engineering of the fungal P450 monooxygenase CYP5136A3 to improve its oxidizing activity toward polycyclic aromatic hydrocarbons
    Khajamohiddin Syed
    Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267 0056, USA
    Protein Eng Des Sel 26:553-7. 2013
    ..L324F also altered the regio-selectivity favoring C position 4 over 9 for hydroxylation of phenanthrene. This is the first instance of engineering a eukaryotic P450 for enhanced oxidation of these fused-ring hydrocarbons. ..
  13. pmc Mitochondria-specific transgenic overexpression of connexin-43 simulates preconditioning-induced cytoprotection of stem cells
    Gang Lu
    Department of Pathology and Lab Medicine, University of Cincinnati, Cincinnati, OH 45220, USA
    Cardiovasc Res 88:277-86. 2010
    ..We posit that these preconditioning effects could be simulated by mitochondria-specific overexpression of Cx-43...
  14. ncbi request reprint Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
    Baoqiang Cao
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, OH 45229, USA
    Bioinformatics 22:303-9. 2006
    ..This offers the possibility of a more reliable estimation of the free parameters in the model with a limited number of experimentally resolved membrane protein structures...
  15. pmc A fungal P450 (CYP5136A3) capable of oxidizing polycyclic aromatic hydrocarbons and endocrine disrupting alkylphenols: role of Trp(129) and Leu(324)
    Khajamohiddin Syed
    Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
    PLoS ONE 6:e28286. 2011
    ..To our knowledge, this is the first report on an AP-oxidizing P450 from fungi and on structure-activity relationship of a eukaryotic P450 for fused-ring PAHs (phenanthrene and pyrene) and AP substrates...
  16. ncbi request reprint Linear regression models for solvent accessibility prediction in proteins
    Michael Wagner
    Division of Biomedical Informatics, Cincinnati Children s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    J Comput Biol 12:355-69. 2005
    ....
  17. ncbi request reprint Combining prediction of secondary structure and solvent accessibility in proteins
    Rafał Adamczak
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, Ohio 45229, USA
    Proteins 59:467-75. 2005
    ..The new method is available through a Web server at http://sable.cchmc.org...
  18. ncbi request reprint Accurate prediction of solvent accessibility using neural networks-based regression
    Rafał Adamczak
    Children s Hospital Research Foundation, Cincinnati, Ohio, USA
    Proteins 56:753-67. 2004
    ..A web server that enables RSA prediction using the new method and provides customizable graphical representation of the results is available at http://sable.cchmc.org...