Alexander L Perryman

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA
    Alexander L Perryman
    Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093 0365, USA
    J Med Chem 45:5624-7. 2002
  2. pmc HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
    Alexander L Perryman
    University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, USA
    Protein Sci 13:1108-23. 2004
  3. ncbi request reprint Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design
    Alexander L Perryman
    Howard Hughes Medical Institute, Center for Theoretical Biological Physics, and Department of Pharmacology, University of California at San Diego, La Jolla, 92093 0365, USA
    Biopolymers 82:272-84. 2006
  4. ncbi request reprint The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    Jung Hsin Lin
    Howard Hughes Medical Institute, Department of Chemistry, University of California at San Diego, 9500 Gilman Dr La Jolla, CA 92093 0365, USA
    Biopolymers 68:47-62. 2003
  5. ncbi request reprint Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design
    Alexander L Perryman
    Howard Hughes Medical Institute, Center for Theoretical Biological Physics and Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Chem Biol Drug Des 67:336-45. 2006
  6. pmc Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease
    Ying Chuan Lin
    Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Acta Crystallogr D Biol Crystallogr 67:540-8. 2011
  7. pmc Fragment-based screen against HIV protease
    Alexander L Perryman
    Department of Molecular Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
    Chem Biol Drug Des 75:257-68. 2010
  8. ncbi request reprint Computational drug design accommodating receptor flexibility: the relaxed complex scheme
    Jung Hsin Lin
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, 92093 0365, USA
    J Am Chem Soc 124:5632-3. 2002
  9. pmc Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge
    Alexander L Perryman
    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
    J Comput Aided Mol Des 28:429-41. 2014

Collaborators

Detail Information

Publications9

  1. ncbi request reprint AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA
    Alexander L Perryman
    Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093 0365, USA
    J Med Chem 45:5624-7. 2002
    ..By analyzing the phosphates of the docked dinucleotides, we developed a model indicating where the viral cDNA and human DNA bind to the integrase core domain...
  2. pmc HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
    Alexander L Perryman
    University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, USA
    Protein Sci 13:1108-23. 2004
    ..In addition, correlated fluctuations in the active site and periphery were noted that point to a possible binding site for allosteric inhibitors...
  3. ncbi request reprint Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design
    Alexander L Perryman
    Howard Hughes Medical Institute, Center for Theoretical Biological Physics, and Department of Pharmacology, University of California at San Diego, La Jolla, 92093 0365, USA
    Biopolymers 82:272-84. 2006
    ..These simulations supported our hypothesis of the mechanism governing flap motion, and they are the first step towards validating that peripheral surface as a new target for drug design...
  4. ncbi request reprint The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    Jung Hsin Lin
    Howard Hughes Medical Institute, Department of Chemistry, University of California at San Diego, 9500 Gilman Dr La Jolla, CA 92093 0365, USA
    Biopolymers 68:47-62. 2003
    ..The MM/PBSA scorings consistently indicate that the calculated binding modes that are most similar to those observed in the x-ray crystallographic complexes are the ones with the lowest free energies...
  5. ncbi request reprint Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design
    Alexander L Perryman
    Howard Hughes Medical Institute, Center for Theoretical Biological Physics and Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Chem Biol Drug Des 67:336-45. 2006
    ....
  6. pmc Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease
    Ying Chuan Lin
    Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Acta Crystallogr D Biol Crystallogr 67:540-8. 2011
    ..The chimeric PR exhibits a comparable number of hydrogen bonds, electrostatic interactions and hydrophobic contacts with DRV and LPV as in the corresponding HIV PR complexes, consistent with IC(50) values in the nanomolar range...
  7. pmc Fragment-based screen against HIV protease
    Alexander L Perryman
    Department of Molecular Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
    Chem Biol Drug Des 75:257-68. 2010
    ....
  8. ncbi request reprint Computational drug design accommodating receptor flexibility: the relaxed complex scheme
    Jung Hsin Lin
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, 92093 0365, USA
    J Am Chem Soc 124:5632-3. 2002
    ..This new method serves as the computational analog of the experimental "SAR by NMR" and "tether" methods, which permit a building block approach for constructing a very potent drug...
  9. pmc Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge
    Alexander L Perryman
    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
    J Comput Aided Mol Des 28:429-41. 2014
    ....