- Knut Teigen, teigen@scripps.edu, post-doctoral
visitor from Bergen, Noway, studying cylic-AMP-dependent protein kinases.
- Mike Crowley, crowley@scripps.edu,
staff scientist, worked on Amber and CHARMM development, and a variety of
other scientific programming tasks. Now at the National Renewable Energy Lab
in Golden, Colorado.
- Wei Zhang, zweig@scripps.edu,
post-doc who worked on path-integral molecular dynamics, and on a new
front-end to the Amber simulation programs. Now at the University of
Texas--Houston Medical School.
- Qizhi Cui, Qizhi.Cui@bri.nrc.ca,
post-doc, working on comparing molecular dynamics simulations to NMR
relaxation results, and on coarse-grained models of ribosome assembly.
Now at the National Research Council of Canada.
- Devleena Shivakumar, devleena@gmail.com, post-doc,
who worked to integrate Amber implicit solvent models into evaluations of
protein-ligand dockings. Now at the University of Chicago.
- John Mongan, jmongan@scripps.edu, M.D./Ph.D.
student from UCSD, who is working on implicit solvent simulations and novel ways
to model pH-dependent behavior in macromolecules. John has completed his
Ph.D. studies, and is returning to finish medical studies as well.
- Seongho Moon, moons@scripps.edu,
post-doc, worked on computational aspects of biomolecular NMR, including
QM/MM analyses of chemical shifts and anisotropies. Now at Samsung Research
Laboratories, Korea.
- Ross Walker, rcw@scripps.edu,
post-doc, worked on making connections between fast optical dynamics, NMR
and molecular dynamics simulations, and QM/MM implementation. Now at the San
Diego Supercomputer Center.
- Francois Dupradeau, fduprado@scripps.edu,
research associate and visitor from Universite de Picardie Jules Verne,
in Amiens, studied electrostatic interactions in proteins and nucleic
acids.
- Rhonda Torres, torres@scripps.edu,
post-doc, used using quantum chemistry and continuum solvation methods to
study active sites of metallo-enzymes. Now at Merck & Co., New Jersey.
- Paramita Dasgupta, Dasgupta.Paramita@mayo.edu, post-doc,
used using molecular dynamics simulations to study NMR relaxation in proteins.
Now at the Mayo Clinic in Rochester, Minnesota.
- Dave Mathews, David_Mathews@urmc.rochester.edu, studied
conformational transitions in RNA, and aspects of RNA secondary structure
prediction. Dave has implemented the nudged elastic band model into Amber,
and developed some new partition-function-based algorithms for RNA secondary
structure analysis. Now on the faculty at the University of Rochester.
- Alexey Onufriev, onufriev@cs.vt.edu,
post-doc who developed implicit solvation models. Now on the faculty
in the computer science department(!) at Virginia Tech.
- Holger Gohlke, gohlke@bioinformatik.uni-frankfurt.de,
post-doc,
looked at energetics of protein-protein and protein-ligand association.
Now on the faculty at J.W. Goethe-Universität in Frankfurt.
- Jens Carlsson, jeca7904@hotmail.com, graduate
student from Sweden, who worked on pK calculations in proteins. Now a Ph.D.
student in Uppsala.
- Tim Meyer, meyerti@scripps.edu,
graduate student in Biotechnology at the Université Louis Pasteur
in Strasbourg, worked doing a research project on structure and dynamics of
tRNA. Now a Ph.D. student in Barcelona.
- Tiqing Liu, liut@scripps.edu, post-doc,
who
explored quantum chemistry approaches to energetics and solvation effects
in transition-metal complexes of biochemical interest. Now at Montana State
University.
- Fahmi Himo, himo@theochem.kth.se,
post-doc, who worked on
quantum chemistry approaches to energetics and solvation effects
in radical-containing complexes of biochemical interest. Now on the faculty
at Stockholm University.
- Xiaoping Xu, xpxu@brunham.edu,
post-doc, used quantum chemistry calculations to obtain insights into
chemical shift behavior in proteins and nucleic acids. Now at the Burnham
Institute in La Jolla.
- Georges Mer, mer.georges@mayo.edu,
post-doc, who prepared isotopically-labeled DNA and RNA samples, and
carryied out NMR relaxation and structural studies on oligonucleotide
systems. Now a faculty memeber at the Mayo Clinic in Rochester, Minnesota.
- Hongjun Liu, hongjun@burnham.org,
post-doc, who worked on fitting atomic models to densities derived from
cryo-electron microscopy and low-resolution X-ray diffraction. Now at the
Burnham Institute in La Jolla.
- Tom Macke, macke@scripps.edu,
graduate student and post-doc. Tom developed
the nucleic-acid builder (NAB) molecular modelling package,
the rnamotif program to find RNA sequence motifs, and other
bioinformatics-related software. Now at Telik in South San Francisco.
- Vickie Tsui,,
vtsui@gene.com,
graduate student, who worked on molecular simulations and NMR-based
refinements of nucleic acids and zinc-finger/nucleic acid complexes.
Now at Genentech, South San Francisco.
- Matthias Ullmann, Matthias.Ullmann@iwr.uni-heidelberg.de,
post-doc, who used quantum chemistry and continuum solvation methods to
study electron and proton transport in cytochrome bc1 and related
systems; although worked on fundamental theories of titration behavior in
macromolecules. Now on the faculty at Bayreuth University.
- Vicki Feher, Victoria.Feher@takedasd.com,
post-doc who studied binding of small molecules to RNA.
Now at Takeda San Diego.
- Will Briggs,wbriggs@scripps.edu,
visiting undergraduate from the University of Vermont, is converting our AVS
molecular graphics modules to Data Explorer (openDX). The openDX link at
the left points to Will's work.
- Neill White, nk_white@yahoo.com,
graduate student at San Diego State University, worked on the
development of distance geometry and low-resolution nucleic acid models
in the NAB program environment. Now at Isis Pharmaceuticals in Carlsbad.
His Java-based molecular modeling program "B" is available at
www.scripps.edu/case/Biomer
- Ru-jen Cheng,rjcheng@mail.nchu.edu.tw,
sabbatical visitor from Taiwan, looked at electronic structure
properties of metalloporphyrins and electrostatic interactions in heme
proteins.
- Jian Li,
jli@prdus.jnj.com,
post-doc, worked on quantum chemistry calculations on iron-sulfur and
molybdenum-iron-sulfur clusters in metalloenzymes. Now at Johnson &
Johnson.
- Jarrod Smith,,
jarrod.smith@vanderbilt.edu,
graduate student, who worked on NMR solution structures
of DNA duplexes and drug-DNA complexes. Now an Assistant Professor
at Vanderbilt University in Nashville.
- Jayashree Srinivasan, jsrinivasan@combichem.com,
post-doc, used electrostatics analysis
and other methods to investigate conformational energetics of DNA and RNA
helices and hairpins.
- Annick Dejaegere, annick@esbs1.u-strasbg.fr,
collaborator from Strasbourg, works on theories of chemical shifts in
nucleic acids.
- Doree Sitkoff, sitkoffd@oculus.bms.com,
post-doc, who worked on theories of chemical shifts in proteins
and nucleic acids. Now at Bristol-Myers Squibb in Princeton, NJ.
- Garry Gippert
garrygippert@yahoo.com,
graduate student who developed
a variety of programs for determiation of solution structures of proteins by
NMR, including routines to carry out systematic conformation searches.
More information on the GAP (Geometric Analysis Programs) Garry wrote
can be found by following the link in the menu bar at the left.
Now at Novozymes in Copenhagen.
- Paul Beroza, pberoza@telik.com,
post-doc, studied the Bohr
effect in hemoglobin using Poisson-Boltzmann electrostatic calculations.
His web site
contains information on PEP (Paul's Electrostatics Program) to compute
numerical solutions to the Poisson-Boltzmann equation, and to peptide analysis
programs. Now at Telik, Inc. in South San Francisco.
- Kizhake Soman, ksoman@nmr.utmb.edu,
post-doc who worked on structure determination from
NMR data (Zn finger) and all atom MD simulations of helical peptides in water.
Currently at the University of Texas in Galveston.
Updated on July 23, 2008. Comments to case@scripps.edu