David Baker (biochemist)
Encyclopedia
David Baker is an American biochemist
and computational biologist
who studies methods to predict
the three-dimensional structures
of protein
s. He is a Professor of Biochemistry at the University of Washington
, where he is the principal investigator of the 30+ member Baker laboratory. He is a Howard Hughes Medical Institute
investigator, and is also a member of the United States National Academy of Sciences
.
The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction
, which has been extended to a distributed computing
project called Rosetta@Home
and Foldit
. The project aims to produce structural models for protein complexes
as well as individual polypeptide chains. The Baker group participates regularly and is recognized for expertise in the CASP
structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol.
Members of the Baker group are also active in the field of protein design
; they are recognized as the first group to have designed a protein, known as Top7
, with an entirely novel fold.
Baker did his graduate work in biochemistry at the University of California, Berkeley
in the laboratory of Randy Schekman
, where he worked predominantly on protein transport and trafficking in yeast
. He did his postdoctoral work with David Agard of UCSF.
Although well known for development of methods for computational prediction of protein structure and function, Baker is focused on the use of computational methods to drive experimental assessment of biology and therefore the Baker laboratory maintains an active experimental biochemistry group.
Baker was elected a Fellow of the American Academy of Arts and Sciences
in 2009. He is married to Hannele Ruohola-Baker, another biochemist at UW
. They have two children, Benjamin and Amanda, both of whom are currently attending Garfield High School
in Seattle.
Biochemist
Biochemists are scientists who are trained in biochemistry. Typical biochemists study chemical processes and chemical transformations in living organisms. The prefix of "bio" in "biochemist" can be understood as a fusion of "biological chemist."-Role:...
and computational biologist
Computational biology
Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...
who studies methods to predict
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
the three-dimensional structures
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s. He is a Professor of Biochemistry at the University of Washington
University of Washington
University of Washington is a public research university, founded in 1861 in Seattle, Washington, United States. The UW is the largest university in the Northwest and the oldest public university on the West Coast. The university has three campuses, with its largest campus in the University...
, where he is the principal investigator of the 30+ member Baker laboratory. He is a Howard Hughes Medical Institute
Howard Hughes Medical Institute
Howard Hughes Medical Institute is a United States non-profit medical research organization based in Chevy Chase, Maryland. It was founded by the American businessman Howard Hughes in 1953. It is one of the largest private funding organizations for biological and medical research in the United...
investigator, and is also a member of the United States National Academy of Sciences
United States National Academy of Sciences
The National Academy of Sciences is a corporation in the United States whose members serve pro bono as "advisers to the nation on science, engineering, and medicine." As a national academy, new members of the organization are elected annually by current members, based on their distinguished and...
.
The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
, which has been extended to a distributed computing
Distributed computing
Distributed computing is a field of computer science that studies distributed systems. A distributed system consists of multiple autonomous computers that communicate through a computer network. The computers interact with each other in order to achieve a common goal...
project called Rosetta@Home
Rosetta@home
Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing platform, run by the Baker laboratory at the University of Washington...
and Foldit
Foldit
Foldit is an online puzzle video game about protein folding. The game is part of an experimental research project, and is developed by the University of Washington's Center for Game Science in collaboration with the UW Department of Biochemistry...
. The project aims to produce structural models for protein complexes
Protein-protein docking
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules...
as well as individual polypeptide chains. The Baker group participates regularly and is recognized for expertise in the CASP
CASP
CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994...
structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol.
Members of the Baker group are also active in the field of protein design
Protein design
Protein design is the design of new protein molecules, either from scratch or by making calculated variations on a known structure. The use of rational design techniques for proteins is a major aspect of protein engineering....
; they are recognized as the first group to have designed a protein, known as Top7
Top7
Top7 is an artificial 93-residue protein, classified as a de novo protein since it was designed by Brian Kuhlman and Gautam Dantas in David Baker's laboratory at the University of Washington to have a unique fold not found in nature. The protein was designed ab initio on a computer with the help of...
, with an entirely novel fold.
Baker did his graduate work in biochemistry at the University of California, Berkeley
University of California, Berkeley
The University of California, Berkeley , is a teaching and research university established in 1868 and located in Berkeley, California, USA...
in the laboratory of Randy Schekman
Randy Schekman
Randy W. Schekman is an American cell biologist at the University of California, Berkeley and Editor-in-Chief of Proceedings of the National Academy of Sciences. In 2011 he was announced as the editor of a new high profile open access journal published by the Howard Hughes Medical Institute, the...
, where he worked predominantly on protein transport and trafficking in yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
. He did his postdoctoral work with David Agard of UCSF.
Although well known for development of methods for computational prediction of protein structure and function, Baker is focused on the use of computational methods to drive experimental assessment of biology and therefore the Baker laboratory maintains an active experimental biochemistry group.
Baker was elected a Fellow of the American Academy of Arts and Sciences
American Academy of Arts and Sciences
The American Academy of Arts and Sciences is an independent policy research center that conducts multidisciplinary studies of complex and emerging problems. The Academy’s elected members are leaders in the academic disciplines, the arts, business, and public affairs.James Bowdoin, John Adams, and...
in 2009. He is married to Hannele Ruohola-Baker, another biochemist at UW
UW
-Universities:in Canada* University of Waterloo* University of Windsor* University of Winnipegin Germany* University of Wuppertal* University of Würzburgin Poland* University of Warsaw* University of Wrocławin the United States of America...
. They have two children, Benjamin and Amanda, both of whom are currently attending Garfield High School
Garfield High School (Seattle, Washington)
James A. Garfield High School is a public high school in the Seattle Public Schools district of Seattle, Washington, USA.Located along 23rd Avenue between E. Alder and E. Jefferson Streets in Seattle's urban Central District, Garfield draws students from all over the city...
in Seattle.