Bruce Donald
Encyclopedia
Bruce Randall Donald is an American
computer scientist
and computational biologist. He is a Professor of Computer Science and Professor of Biochemistry at Duke University
. He has made numerous contributions to several fields in Computer Science
such as robotics
, Microelectromechanical Systems
(MEMS), Geometric & physical algorithms and computational geometry
; as well as in areas of Structural Molecular Biology & Biochemistry
such as Protein design
, Protein Structure Determination and Computational Chemistry
.
in 1980. After working at the Laboratory for Computer Graphics and Spatial Analysis in the Harvard Graduate School of Design
at Harvard University
, he then attended MIT EECS, where he received his S.M. in EECS (1984) and Ph.D. in Computer Science (1987) under the supervision of professor Tomás Lozano-Pérez in the MIT AI Lab (Artificial Intelligence Laboratory).
He was an associate professor of Computer Science at Cornell University
until 1998, and then was Joan P. and Edward J. Foley Jr 1933 Professor of Computer Science, Dartmouth College
until 2006 when he moved to Duke University
. Currently Donald is the William and Sue Gross Professor of Computer Science, Duke University and Professor of Biochemistry, School of Medicine, Duke University Medical Center.
He is a Fellow
of the Association for Computing Machinery
(ACM) and a Fellow
of the IEEE. Previously, he was a Guggenheim Fellow (2001–2002) and received a National Science Foundation Presidential Young Investigator Award
(1989–1994).
Recently, his research has been in the areas of Structural Molecular Biology; chiefly, Protein Design and Protein Structure Determination from NMR
data. He has developed numerous algorithms for protein design
which has been successfully tested experimentally in the wet lab. The protein design algorithms attempt to incorporate additional molecular flexibility into the design process by using ensembles and continuously-flexible rotamers and backbones. His algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry has been used in the structure determination of the enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis
, an important advancement in Cryptosporidium biology. He has designed many algorithms and computational protocols to extract structural information from NMR data, and use that information to compute structures of globular proteins and symmetric homo-oligomers. A distinct feature of his algorithms is that they use less data, and provide complexity-theoretic guarantees on time and space.
, University of Washington, Seattle, University of Massachusetts, Amherst, Dartmouth College
, Middlebury College
and University of Toronto
; and some are researchers in prestigious research organizations viz. NIAID, NIST, IBM
, Sandia National Laboratories
.
United States
The United States of America is a federal constitutional republic comprising fifty states and a federal district...
computer scientist
Computer scientist
A computer scientist is a scientist who has acquired knowledge of computer science, the study of the theoretical foundations of information and computation and their application in computer systems....
and computational biologist. He is a Professor of Computer Science and Professor of Biochemistry at Duke University
Duke University
Duke University is a private research university located in Durham, North Carolina, United States. Founded by Methodists and Quakers in the present day town of Trinity in 1838, the school moved to Durham in 1892. In 1924, tobacco industrialist James B...
. He has made numerous contributions to several fields in Computer Science
Computer science
Computer science or computing science is the study of the theoretical foundations of information and computation and of practical techniques for their implementation and application in computer systems...
such as robotics
Robotics
Robotics is the branch of technology that deals with the design, construction, operation, structural disposition, manufacture and application of robots...
, Microelectromechanical Systems
Microelectromechanical systems
Microelectromechanical systems is the technology of very small mechanical devices driven by electricity; it merges at the nano-scale into nanoelectromechanical systems and nanotechnology...
(MEMS), Geometric & physical algorithms and computational geometry
Computational geometry
Computational geometry is a branch of computer science devoted to the study of algorithms which can be stated in terms of geometry. Some purely geometrical problems arise out of the study of computational geometric algorithms, and such problems are also considered to be part of computational...
; as well as in areas of Structural Molecular Biology & Biochemistry
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
such as 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....
, Protein Structure Determination and Computational Chemistry
Computational chemistry
Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...
.
Biography
Donald received a B.A. summa cum laude in Russian Language from Yale UniversityYale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
in 1980. After working at the Laboratory for Computer Graphics and Spatial Analysis in the Harvard Graduate School of Design
Harvard Graduate School of Design
The Harvard Graduate School of Design is a graduate school at Harvard University offering degrees in Architecture, Landscape Architecture, and Urban Planning and Design.-History:...
at Harvard University
Harvard University
Harvard University is a private Ivy League university located in Cambridge, Massachusetts, United States, established in 1636 by the Massachusetts legislature. Harvard is the oldest institution of higher learning in the United States and the first corporation chartered in the country...
, he then attended MIT EECS, where he received his S.M. in EECS (1984) and Ph.D. in Computer Science (1987) under the supervision of professor Tomás Lozano-Pérez in the MIT AI Lab (Artificial Intelligence Laboratory).
He was an associate professor of Computer Science at Cornell University
Cornell University
Cornell University is an Ivy League university located in Ithaca, New York, United States. It is a private land-grant university, receiving annual funding from the State of New York for certain educational missions...
until 1998, and then was Joan P. and Edward J. Foley Jr 1933 Professor of Computer Science, Dartmouth College
Dartmouth College
Dartmouth College is a private, Ivy League university in Hanover, New Hampshire, United States. The institution comprises a liberal arts college, Dartmouth Medical School, Thayer School of Engineering, and the Tuck School of Business, as well as 19 graduate programs in the arts and sciences...
until 2006 when he moved to Duke University
Duke University
Duke University is a private research university located in Durham, North Carolina, United States. Founded by Methodists and Quakers in the present day town of Trinity in 1838, the school moved to Durham in 1892. In 1924, tobacco industrialist James B...
. Currently Donald is the William and Sue Gross Professor of Computer Science, Duke University and Professor of Biochemistry, School of Medicine, Duke University Medical Center.
He is a Fellow
Fellow
A fellow in the broadest sense is someone who is an equal or a comrade. The term fellow is also used to describe a person, particularly by those in the upper social classes. It is most often used in an academic context: a fellow is often part of an elite group of learned people who are awarded...
of the Association for Computing Machinery
Association for Computing Machinery
The Association for Computing Machinery is a learned society for computing. It was founded in 1947 as the world's first scientific and educational computing society. Its membership is more than 92,000 as of 2009...
(ACM) and a Fellow
Fellow
A fellow in the broadest sense is someone who is an equal or a comrade. The term fellow is also used to describe a person, particularly by those in the upper social classes. It is most often used in an academic context: a fellow is often part of an elite group of learned people who are awarded...
of the IEEE. Previously, he was a Guggenheim Fellow (2001–2002) and received a National Science Foundation Presidential Young Investigator Award
Presidential Young Investigator Award
The Presidential Young Investigator Award was awarded by the National Science Foundation. The program operated from 1984 to 1991, and was replaced by the NSF Young Investigator Awards and Presidential Faculty Fellows Program...
(1989–1994).
Work
Bruce Donald’s early research was in the field of robotic motion planning and distributed manipulation. Later he has made numerous contributions to MEMS and Micro-robotics, and designed MEMS micro-robots with dimensions of 60 µm by 250 µm by 10 µm.Recently, his research has been in the areas of Structural Molecular Biology; chiefly, Protein Design and Protein Structure Determination from NMR
NMR
NMR may refer to:Applications of Nuclear Magnetic Resonance:* Nuclear magnetic resonance* NMR spectroscopy* Solid-state nuclear magnetic resonance* Protein nuclear magnetic resonance spectroscopy* Proton NMR* Carbon-13 NMR...
data. He has developed numerous algorithms for 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....
which has been successfully tested experimentally in the wet lab. The protein design algorithms attempt to incorporate additional molecular flexibility into the design process by using ensembles and continuously-flexible rotamers and backbones. His algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry has been used in the structure determination of the enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis
Cryptosporidium hominis
Cryptosporidium hominis, along with Cryptosporidium parvum, is among the medically important Cryptosporidium species. It is an obligate parasite of humans that can colonize the gastrointestinal tract resulting in the gastroenteritis and diarrhea characteristic of cryptosporidiosis. Unlike C....
, an important advancement in Cryptosporidium biology. He has designed many algorithms and computational protocols to extract structural information from NMR data, and use that information to compute structures of globular proteins and symmetric homo-oligomers. A distinct feature of his algorithms is that they use less data, and provide complexity-theoretic guarantees on time and space.
Students
Donald has supervised many students and postdocs, many of whom are now professors in reputed universities such as MIT, CMUCMU
CMU may stand for a university:*Carnegie Mellon University in Pittsburgh, Pennsylvania, United States*Central Michigan University in Mount Pleasant, Michigan, United States*Canadian Mennonite University in Winnipeg, Manitoba, Canada...
, University of Washington, Seattle, University of Massachusetts, Amherst, Dartmouth College
Dartmouth College
Dartmouth College is a private, Ivy League university in Hanover, New Hampshire, United States. The institution comprises a liberal arts college, Dartmouth Medical School, Thayer School of Engineering, and the Tuck School of Business, as well as 19 graduate programs in the arts and sciences...
, Middlebury College
Middlebury College
Middlebury College is a private liberal arts college located in Middlebury, Vermont, USA. Founded in 1800, it is one of the oldest liberal arts colleges in the United States. Drawing 2,400 undergraduates from all 50 United States and over 70 countries, Middlebury offers 44 majors in the arts,...
and University of Toronto
University of Toronto
The University of Toronto is a public research university in Toronto, Ontario, Canada, situated on the grounds that surround Queen's Park. It was founded by royal charter in 1827 as King's College, the first institution of higher learning in Upper Canada...
; and some are researchers in prestigious research organizations viz. NIAID, NIST, IBM
IBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
, Sandia National Laboratories
Sandia National Laboratories
The Sandia National Laboratories, managed and operated by the Sandia Corporation , are two major United States Department of Energy research and development national laboratories....
.
Publications
Donald is the author of over 100 publications. A representative selection:- Kinodynamic Motion Planning. Bruce Randall Donald, Patrick G. Xavier, John F. Canny, John H. Reif. J. ACM 40(5): 1048-1066 (1993).
- Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase. Robert H. O’Neil, Ryan H. Lilien, Bruce R. Donald, Robert M. Stroud and Amy C. Anderson. J Biol Chem 2003. 278(52):52980-7.
- A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry. Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald. Acta Crystallogr D Biol Crystallogr. 2004.60(Pt 6):1057-67.
- A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data. Lincong Wang, Ramgopal R. Mettu and Bruce R. Donald. Journal of Computational Biology 2006; 13(7): 1276-1288.
- Structure Determination of Symmetric Homo-oligomers by a Complete Search of Symmetry Configuration Space Using NMR Restraints and van der Waals Packing. S. Potluri, A. Yan, J. Chou, Bruce R. Donald and C. Bailey-Kellogg. Proteins 2006; 65(1):203-219.
- The Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. Ivelin Georgiev, Ryan H. Lilien and Bruce R. Donald. Journal of Computational Chemistry 2008;29(10):1527-42.
- Computational structure-based redesign of enzyme activity. Cheng-Yu Chen, Ivelin Georgiev, Amy C. Anderson and Bruce R. Donald. Proceedings of the National Academy of Sciences (PNAS) U.S.A. 2009;106(10):3764-9.
- High-Resolution Protein Structure Determination Starting with a Global Fold Calculated from Exact Solutions to the RDC Equations. J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan, P. Zhou and Bruce R. Donald. Journal of Biomolecular NMRJournal of Biomolecular NMRThe Journal of Biomolecular NMR publishes research on technical developments and innovative applications of nuclear magnetic resonance spectroscopy for the study of structure and dynamic properties of biopolymers in solution, liquid crystals, solids and mixed environments....
2009; 45(3):265-281