Alexander L Perryman
Affiliation: University of California
- AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNAAlexander 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...
- 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 drugsAlexander 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...
- Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug designAlexander 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...
- The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring schemeJung 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...
- 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 designAlexander 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....
- Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV proteaseYing 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...
- Fragment-based screen against HIV proteaseAlexander 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....
- Computational drug design accommodating receptor flexibility: the relaxed complex schemeJung 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...
- 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 challengeAlexander 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....