Sara E Nichols

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface
    Sara E Nichols
    Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093 0365, USA
    Protein Sci 22:745-54. 2013
  2. pmc Rational prediction with molecular dynamics for hit identification
    Sara E Nichols
    Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
    Curr Top Med Chem 12:2002-12. 2012
  3. pmc Predictive power of molecular dynamics receptor structures in virtual screening
    Sara 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
  4. doi On the use of molecular dynamics receptor conformations for virtual screening
    Sara E Nichols
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 819:93-103. 2012
  5. pmc Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC
    Meekyum Olivia Kim
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    J Comput Aided Mol Des 27:235-46. 2013
  6. pmc Activation and dynamic network of the M2 muscarinic receptor
    Yinglong Miao
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 110:10982-7. 2013
  7. doi Thermodynamic integration to predict host-guest binding affinities
    Morgan Lawrenz
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    J Comput Aided Mol Des 26:569-76. 2012
  8. pmc Identification of potential small molecule binding pockets on Rho family GTPases
    Juan Manuel Ortiz-Sánchez
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 7:e40809. 2012
  9. doi Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
    Yinglong Miao
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093, USA
    Phys Chem Chem Phys 16:6398-406. 2014
  10. ncbi Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor
    Yinglong Miao
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA
    Chem Biol Drug Des 83:237-46. 2014

Collaborators

Detail Information

Publications11

  1. pmc Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface
    Sara E Nichols
    Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093 0365, USA
    Protein Sci 22:745-54. 2013
    ..Furthermore, this method may be applied to any protein-protein interaction...
  2. pmc Rational prediction with molecular dynamics for hit identification
    Sara E Nichols
    Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
    Curr Top Med Chem 12:2002-12. 2012
    ..With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline...
  3. pmc Predictive power of molecular dynamics receptor structures in virtual screening
    Sara 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...
  4. doi On the use of molecular dynamics receptor conformations for virtual screening
    Sara E Nichols
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 819:93-103. 2012
    ..Here we highlight some details and nuances of using such snapshots and evaluating them for predictive performance...
  5. pmc Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC
    Meekyum Olivia Kim
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    J Comput Aided Mol Des 27:235-46. 2013
    ....
  6. pmc Activation and dynamic network of the M2 muscarinic receptor
    Yinglong Miao
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 110:10982-7. 2013
    ..Together with the finding that residue motions in the ligand-binding and G-protein-coupling sites of the apo receptor are correlated, this result highlights a dynamic network for allosteric regulation of the M2 receptor activation. ..
  7. doi Thermodynamic integration to predict host-guest binding affinities
    Morgan Lawrenz
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    J Comput Aided Mol Des 26:569-76. 2012
    ..Overall, we show that charged host-guest systems studied here, initialized in unconfirmed docking poses, present a challenge to accurate alchemical simulation methods...
  8. pmc Identification of potential small molecule binding pockets on Rho family GTPases
    Juan Manuel Ortiz-Sánchez
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 7:e40809. 2012
    ....
  9. doi Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
    Yinglong Miao
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093, USA
    Phys Chem Chem Phys 16:6398-406. 2014
    ..50)-Glu(6.30) ionic lock, the Trp(6.48) toggle switch and the hydrogen interactions between Tyr(5.58)-Tyr(7.53). ..
  10. ncbi Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor
    Yinglong Miao
    Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA
    Chem Biol Drug Des 83:237-46. 2014
    ..They serve as promising target sites for designing novel allosteric modulators as receptor-selective drugs. ..
  11. pmc Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria
    Tina Dasgupta
    Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
    ACS Chem Biol 4:29-40. 2009
    ..To our knowledge, these are the first co-crystal structures of novel, biguanide, non-WR99210 compounds that are active against folate-resistant malaria parasites in cell culture...