Publications



Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|
J Chem Theory Comput 2013 Sep 1;9(9):4195-4204. Epub 2013 Aug 1.
Department of Mathematics and Center for Theoretical Biological Physics, University of California , San Diego, La Jolla, California 92093-0112, United States.


On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations.
J Chem Theory Comput 2013 Jan 26;9(1):46-53. Epub 2012 Oct 26.
Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093-0365, United States ; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California 92093, United States.

Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties.
J Chem Theory Comput 2009 Dec;5(12):3150-3160
Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365 and Laboratory of Physical Chemistry, ETHZ, ETH Hönggerberg, CH 8093, Zürich, Switzerland.

Multiple pathways guide oxygen diffusion into flavoenzyme active sites.
Proc Natl Acad Sci U S A 2009 Jun 16;106(26):10603-8. Epub 2009 Jun 16.
Department of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir.
J Chem Theory Comput 2009 Apr 25;5(4):1106-1116. Epub 2009 Mar 25.
Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365.

E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study.
J Phys Chem B 2008 Dec;112(51):16802-14
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.

Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association.
Proc Natl Acad Sci U S A 2008 May 21;105(21):7456-61. Epub 2008 May 21.
Departments of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.


The GROMOS software for biomolecular simulation: GROMOS05.
J Comput Chem 2005 Dec;26(16):1719-51
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.



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