Valerie Daggett

Last updated
Valerie D. Daggett
EducationUniversity of California, San Francisco
Known forLarge-scale simulations of protein folding
Scientific career
Institutions Stanford University
Thesis Molecular modelling of peptides and proteins  (1990)
Doctoral advisor Irwin Kuntz, Peter Kollman
Other academic advisors Michael Levitt

Valerie Daggett is a professor of bioengineering at the University of Washington in Seattle, Washington, United States.

Contents

Education and career

Daggett has a B.S. from Reed College. She received her Ph.D. from the University of California, San Francisco, advised by Irwin Kuntz and Peter Kollman, and subsequently held a postdoctoral position at Stanford University with Michael Levitt, a co-recipient of the 2013 Nobel Prize in Chemistry. [1]

As of 2021, she is also the chief executive officer of AltPep, a biomedical startup that was a spinoff from her research at the University of Washington. [2]

Research

Her laboratory focuses on work in molecular dynamics simulations of proteins and other biomolecules. Daggett is well known for large-scale simulations of protein folding, especially unfolding, and native state dynamics through her "dynameomics" project. [3] [4] In 2005, the Daggett laboratory was awarded a supercomputing grant by the U.S. Department of Energy, which was renewed for almost two million processor-hours in 2006; [5] the group has also participated in Microsoft Research high-performance computing projects. [6]

Awards and honors

In 2011, Daggett was named a fellow of the Biophysical Society. [7] Daggett was one of two University of Washington scientists named 2015 American Institute for Medical and Biological Engineering fellows. [8]

Related Research Articles

<span class="mw-page-title-main">Molecular dynamics</span> Computer simulations to discover and understand chemical properties

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.

Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.

<span class="mw-page-title-main">Systems science</span> Study of the nature of systems

Systems science, also referred to as systems research, or, simply, systems, is a transdisciplinary field that is concerned with understanding simple and complex systems in nature and society, which leads to the advancements of formal, natural, social, and applied attributions throughout engineering, technology and science, itself.

<span class="mw-page-title-main">Force field (chemistry)</span> Concept on molecular modeling

In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system on the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference being that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates.

<span class="mw-page-title-main">Michael Levitt (biophysicist)</span> Nobel laureate, biophysicist, and professor of structural biology (born 1947)

Michael Levitt, is a South African-born biophysicist and a professor of structural biology at Stanford University, a position he has held since 1987. Levitt received the 2013 Nobel Prize in Chemistry, together with Martin Karplus and Arieh Warshel, for "the development of multiscale models for complex chemical systems". In 2018, Levitt was a founding co-editor of the Annual Review of Biomedical Data Science.

<span class="mw-page-title-main">Martin Karplus</span> Austrian-born American theoretical chemist

Martin Karplus is an Austrian and American theoretical chemist. He is the Director of the Biophysical Chemistry Laboratory, a joint laboratory between the French National Center for Scientific Research and the University of Strasbourg, France. He is also the Theodore William Richards Professor of Chemistry, emeritus at Harvard University. Karplus received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Arieh Warshel, for "the development of multiscale models for complex chemical systems".

<span class="mw-page-title-main">Harry B. Gray</span> American inorganic chemist

Harry Barkus Gray is the Arnold O. Beckman Professor of Chemistry at California Institute of Technology.

<span class="mw-page-title-main">Jennifer Lippincott-Schwartz</span> American biologist

Jennifer Lippincott-Schwartz is a Senior Group Leader at Howard Hughes Medical Institute's Janelia Research Campus and a founding member of the Neuronal Cell Biology Program at Janelia. Previously, she was the Chief of the Section on Organelle Biology in the Cell Biology and Metabolism Program, in the Division of Intramural Research in the Eunice Kennedy Shriver National Institute of Child Health and Human Development at the National Institutes of Health from 1993 to 2016. Lippincott-Schwartz received her PhD from Johns Hopkins University, and performed post-doctoral training with Richard Klausner at the NICHD, NIH in Bethesda, Maryland.

Bernhard Örn Pálsson is the Galletti Professor of Bioengineering and an adjunct professor of Medicine at the University of California, San Diego.

Linda Carol Hsieh-Wilson is an American chemist and the Milton and Rosalind Chang Professor of Chemistry at the California Institute of Technology. She is known for her work in chemical neurobiology on understanding the structure and function of carbohydrates in the nervous system. Her studies have revealed critical roles for carbohydrates and protein glycosylation in fundamental processes ranging from cellular metabolism to memory storage. She is a member of the American Academy of Arts and Sciences and was elected to the National Academy of Sciences in 2022.

<span class="mw-page-title-main">Martin Gruebele</span>

Martin Gruebele is a German-born American physical chemist and biophysicist who is currently James R. Eiszner Professor of Chemistry, Professor of Physics, Professor of Biophysics and Computational Biology at the University of Illinois Urbana-Champaign, where he is the principal investigator of the Gruebele Group.

Naomi Shauna Ginsberg is a Canadian electrical engineer, physicist, and scientist. She is currently an associate professor of chemistry at the University of California, Berkeley.

Stephen H. White is an American Biophysicist, academic, and author. He is a Professor Emeritus of Physiology and Biophysics at the University of California, Irvine.

<span class="mw-page-title-main">Sarah Teichmann</span> German bioinformatician

Sarah Amalia Teichmann is a German scientist who is head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, at the University of Cambridge and a senior research fellow at Churchill College, Cambridge.

<span class="mw-page-title-main">Rong Li</span> American cell biologist (born 1967)

Rong Li is the Director of Mechanobiology Institute, a Singapore Research Center of Excellence, at the National University of Singapore. She is a Distinguished Professor at the National University of Singapore's Department of Biological Sciences and Bloomberg Distinguished Professor of Cell Biology and Chemical & Biomolecular Engineering at the Johns Hopkins School of Medicine and Whiting School of Engineering. She previously served as Director of Center for Cell Dynamics in the Johns Hopkins School of Medicine’s Institute for Basic Biomedical Sciences. She is a leader in understanding cellular asymmetry, division and evolution, and specifically, in how eukaryotic cells establish their distinct morphology and organization in order to carry out their specialized functions.

Teresa Lyn Head-Gordon is an American chemist and the Chancellor's Professor of Chemistry, Bioengineering, and Chemical and Biomolecular Engineering at the University of California, Berkeley. She is also a faculty scientist in the Chemical Sciences Division at the Lawrence Berkeley National Laboratory and a fellow of both the American Institute for Medical and Biological Engineering and the American Chemical Society (ACS).

<span class="mw-page-title-main">Amalie Frischknecht</span> American theoretical polymer physicist

Amalie L. Frischknecht is an American theoretical polymer physicist at Sandia National Laboratories in Albuquerque, New Mexico. She was elected a fellow of the American Physical Society (APS) in 2012 for "her outstanding contributions to the theory of ionomers and nanocomposites including the development and application of density functional theory to polymers". Her research focuses on understanding the structure, phase behavior, and self-assembly of polymer systems, such as complex fluids polymer nanocomposites, lipid bilayer assemblies, and ionomers.

Collin M. Stultz is an American biomolecular engineer, physician-scientist and academic at the Massachusetts Institute of Technology and the Massachusetts General Hospital. He is the Nina T. and Robert H. Rubin Professor in Medical Engineering and Science at MIT, a Professor of Electrical Engineering and Computer Science also at MIT, a faculty member in the Harvard-MIT Division of Health Sciences and Technology, and a cardiologist at the Massachusetts General Hospital. He is also co-Director of the Harvard–MIT Program in Health Sciences and Technology

<span class="mw-page-title-main">Backbone-dependent rotamer library</span> Collection of data on conformations of a given proteins amino acid side chains

In biochemistry, a backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations of the amino acid side chains in proteins as a function of the backbone dihedral angles φ and ψ of the Ramachandran map. By contrast, backbone-independent rotamer libraries express the frequencies and mean dihedral angles for all side chains in proteins, regardless of the backbone conformation of each residue type. Backbone-dependent rotamer libraries have been shown to have significant advantages over backbone-independent rotamer libraries, principally when used as an energy term, by speeding up search times of side-chain packing algorithms used in protein structure prediction and protein design.

<span class="mw-page-title-main">Yu-Shan Lin</span> Taiwanese chemist

Yu-Shan Lin is a computational chemist. She is an associate professor of chemistry at Tufts University in the United States. Her research lab uses computational chemistry to understand and design biomolecules, with topics focusing on cyclic peptides, protein folding, and collagen.

References

  1. Daggett, Valerie. "Daggett Research Group" . Retrieved 10 February 2015.
  2. "Team | AltPep". www.altpep.com. Retrieved 2021-11-17.
  3. Doerr, Alison (2010). "A database of dynamics". Nature Methods. 7 (6): 426. doi: 10.1038/nmeth0610-426 . PMID   20524218.
  4. Van Der Kamp, M. W.; Schaeffer, R. D.; Jonsson, A. L.; Scouras, A. D.; Simms, A. M.; Toofanny, R. D.; Benson, N. C.; Anderson, P. C.; Merkley, E. D.; Rysavy, S.; Bromley, D.; Beck, D. A. C.; Daggett, V. (2010). "Dynameomics: A Comprehensive Database of Protein Dynamics". Structure. 18 (4): 423–435. doi:10.1016/j.str.2010.01.012. PMC   2892689 . PMID   20399180.
  5. DOE press release on the awarding of INCITE grants. 22 Dec 2004. Access date 17 Jan 2007.
  6. Microsoft Corporation. "GrayWulf Takes Byte Out of Data Overload". Microsoft Research. Retrieved 10 February 2015.
  7. "2 0 1 9 H I S T O R I C A L I N F O R M A T I O N" (PDF). Retrieved November 17, 2021.
  8. Wright, Laura Elizabeth (26 January 2015). "Suzie Pun and Valerie Daggett elected AIMBE Fellows". University of Washington Department of Engineering. Retrieved 10 February 2015.