Affiliation: University of California
- Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulationsAnthony Ivetac
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0365, USA
J Mol Biol 388:644-58. 2009..From a methodological point of view, our results suggest that the multicopy MD simulation approach is very useful when studying proteins that perform such large conformational changes...
- Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approachAnthony Ivetac
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
Chem Biol Drug Des 76:201-17. 2010..This mapping data can now serve to drive a combination of fragment-based and virtual screening approaches for the discovery of small molecules that bind at these sites and which may offer highly selective therapies...
- Molecular recognition in the case of flexible targetsAnthony Ivetac
Department of Chemistry and Biochemistry University of California San Diego, La Jolla, CA 92093 0365, USA
Curr Pharm Des 17:1663-71. 2011..We also discuss some encouraging developments, aimed at addressing current weaknesses of the RCS...
- A molecular dynamics ensemble-based approach for the mapping of druggable binding sitesAnthony Ivetac
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
Methods Mol Biol 819:3-12. 2012..This approach has recently been applied to a pair of human G-protein-coupled receptors (GPCRs), resulting in the detection of five potential allosteric sites...
- Predictive power of molecular dynamics receptor structures in virtual screeningSara E Nichols
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, United States
J Chem Inf Model 51:1439-46. 2011..Additionally, MD can move conformations previously not amenable to docking into the predictive range...
- Characterization of a clinical polymer-drug conjugate using multiscale modelingLili X Peng
Department of Bioengineering, University of California, San Diego, CA, USA
Biopolymers 93:936-51. 2010..This multiscale modeling approach may be advantageous for the design of cancer therapeutic delivery systems. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 936-951, 2010...