- Outsmarting HIV With Vaccine Antigens Made to
Order, Duke News (2015).
- An HIV vaccine research team led by scientists from the National
Institutes of Health has engineered a protein to maintain the
particular shape predicted to be most effective at stimulating the
immune system to produce powerful antibodies against the virus. The
work was led by John R. Mascola, M.D., and Peter D. Kwong, Ph.D., of
the Vaccine Research Center (VRC) at the National Institute of Allergy
and Infectious Diseases (NIAID), part of NIH. The team
included Dlab (Donald Lab)
members Mark Hallen
and Bruce Donald, and former
Dlab PhD (2009) Ivelin Georgiev (now
at the VRC).
One way HIV hides from the immune system is by continuously changing
the shape of a surface molecule where powerful antibodies could
potentially bind to stop infection. This shape-shifting of the
so-called viral spike helps conceal key antibody-binding sites and
instead exposes other sites on the virus that lure minimally effective
In previous work, scientists found that an
effective HIV vaccine that teaches the immune system to neutralize the
virus should be based on a particular form of the viral spike called
the closed, pre-fusion configuration. In the new research, we report
the stabilization of a protein that maintains this very configuration
and confirm that it allows binding of effective antibodies but not
In addition, while the viral spike typically changes shape in the
presence of a common immune-cell receptor called CD4, the newly
stabilized protein does not. This is critical because the protein
needs to stay in the closed, pre-fusion configuration to elicit potent
antibodies that broadly neutralize HIV.
More molecular work remains to overcome other
hurdles to eliciting HIV antibodies that could stop most strains of
the virus from causing infection.
- Mark Hallen won a Liebmann
Graduate Research Fellowship for his work in the Donald Lab on protein
design algorithms and HIV (2015).
- Our paper Systematic solution to homoöligomeric structures
determined by NMR
Using computational algorithms and experimental evolution,
researchers are predicting antimicrobial-resistance patterns to
improve drug design. The Scientist (2015).
Ahead of Antibiotic-resistant Bacteria UCONN Today (2015).
Pablo Gainza in a TIME Magazine article on research by the Donald
Predicts Antibiotic Resistances, Buying Us More Time. Nature
World News, 2015.
fight drug resistance with software. Duke Chronicle, 2015.
UConn Researchers Use Protein Design Algorithms to Predict
Potential Resistance Mutations in MRSA. Genomeweb, 2015.
- Predicting superbugs' countermoves to new drugs:
Software predicts MRSA'S response to new drug before it's tested on
patients. Duke Today, 2015.
- Mark Hallen received the best poster award at the Fall 2014 Biochemistry Department retreat for his poster entitled "Computational Design of Probes and Antibodies using EPIC and COMETS."
- Jeff Martin was presented the Department of Computer Science's Outstanding PhD Award for his thesis, "Geometric Algorithms for Protein Structure Determination Using Measurements from NMR Spectroscopy," at the department's annual meeting.
- Kyle Roberts and Bruce Donald won the best poster award at the ISMB 3DSIG conference in Boston for their poster entitled "Improving Minimized Protein Design with Partitioned Continuous Rotamers" (2014).
Ojewole won an NSF Graduate Research Fellowship for his work in
the Donald Lab on protein design algorithms and infectious
Nisonoff received a DSRF Fellowship for his work in the Donald Lab
on protein design and HIV vaccine design (2014).
Gainza just completed an internship at the Vaccine Research Center
(VRC) at NIAID/NIH, where he worked on collaborative projects between
the Donald Lab and the VRC related to HIV antibodies (2014).
Hallen will do an internship this summer at the Vaccine Research
Center (VRC) at NIAID/NIH, working on collaborative projects between
the Donald Lab and the VRC related to HIV antibodies (2014).
- NIH has funded our competing renewal R01 application for research in
Computational Structure-Based Protein Design (2014).
Martin, Pei Zhou,
Donald received the best poster award at the 2014 Biochemistry
Department Symposium for their poster entitled "Systematic Solution to
Homo-oligomeric Structures Determined by NMR."
- Most Donald Lab MEMS and Robot movies are now available on
- Computer scientist in profile:
Bruce R. Donald. By Amarda Shehu, ACM SIGBioinformatics
Protein May Help HIV Vaccine Development. Combining expertise
in biochemistry, immunology and advanced computation, researchers
at Duke University have determined the structure of a key part of
the HIV envelope protein, the gp41 membrane proximal external
region (MPER), which previously eluded detailed structural
description. Duke News, 2014.
in on HIV. Spectroscopy Now 2014.
Against HIV. UNC TV 2014.
Probe Gives a Single Neuron's View of Brain Activity.
Technology Review (2013).
Electrodes Spear Nerve Cells
(Scientists use ultrafine electrodes made from carbon nanotubes to
record nerve cell firing in mouse brains). Chemical &
Engineering News (2013).
mirror of article]
scientists designed a thin, flexible carbon-nanotube spear
to study individual brain cells. Duke News (2013).
nanotube harpoon catches individual brain-cell signals.
Eureka Alert (2013).
look into Duke's scientific research: The Donald Lab
uses advanced technologies to solve
biomedical problems. Duke Chronicle (2013).
- Cheng-Yu Chen et al. received the best poster award at the
Fall 2012 Biochemistry Department retreat for their poster titled "NMR
Structure Determination of GrsA Epimerase Domain by Residual Dipolar
Couplings (RDCs), Sparse NOEs and PREs." The poster was co-authored by
Cheng-Yu Chen, Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou and
Bruce R. Donald.
- Bruce Donald gave a talk, "Protein Interface Design, Cystic Fibrosis and HIV," in the Duke CBB Computational Biology Seminar on September 17, 2012.
Algorithms Aid Search for Cystic Fibrosis Drugs,
NIH NIGMS Biomedical Beat (Research Digest) May 17 Issue (2012).
Design Leads To Cystic Fibrosis Drug Candidates
& Engineering News, 2012).
- Bruce Donald was named James
B. Duke Professor (May, 2012: Duke
Announces Distinguished Professors and July, 2012: Duke Computer Science news article).
Molecules Point to New Therapy for Cystic Fibrosis, Duke
- Our paper is the Cover
for PROTEINS, February 2012 issue. Please see:
Protein Loop Closure Using Orientational Restraints from NMR Data.
C.Tripathy, J.Zeng, P.Zhou, and B.R.Donald.* Proteins:
Structure, Function, and Bioinformatics 2012; 80(2):433-453.
This work describes an advance in methodology for the structure
determination of protein loops by NMR, using residual dipolar
- D-Lab Ph.D. student Mark Hallen was awarded a prestigious PhRMA Foundation graduate
fellowship. The goal of the fellowship Program is to promote the use
of informatics in an integrative approach to the understanding of
biological and disease processes. Fellowship awards support career
development for scientists engaged in cutting-edge research in
information technology and experimental validation, thus advancing the
integration of molecular and clinical approaches into problems of
pharmacological concern (December, 2011).
- Recent Donald Lab ("D-Lab") Alumni news:
What else happened lately?
- Bruce Donald was featured in the Spring 2011 issue of Stanford's Profiles in Computer Science Courage. (Also available here)
- In 2011, Bruce Donald was elected Fellow of the
- From 2000-2011 we have had 11 papers accepted in the RECOMB
conference, which we enjoy going to. On most years that's one paper
but in 2011 we had 4 papers accepted for oral presentation and the
proceedings. They are listed here on our
- An article on the Donald Lab's work (in collaboration with Amy
Anderson's group) on predicting resistance mutations using protein
design algorithms appeared in PNAS in July 2010, and was
reported by DukeHealth,
EurekAlert, the News
& Observer, and
- In 2009, Bruce Donald was elected Fellow of
- Congratulations to Ivelin Georgiev and Jeff Martin, recipients of awards announced at the Department of Computer Science Annual Meeting in August 2009. Ivelin was named winner of the Outstanding Ph.D. Dissertation Award and Nomination for the ACM Dissertation Award for his thesis entitled "Novel Algorithms for Computational Protein Design with Applications to Enzyme Redesign and Small-Molecule Inhibitor Design." Jeff was presented the Outstanding Master's Thesis Award for his thesis entitled "Algorithms for Structure Determination of Symmetric Proteins from Nuclear Magnetic Resonance Data."
- Protein Power, an article in SeedMagazine.com, in April 2009, recognized the Donald Lab's work in enzyme engineering.
- The Donald Lab's work in using computer algorithms to redesign enzymes that make antibiotics was reported in IEEE Spectrum Online in the article Computer-Designed Drugs Could Thwart Antibiotic-Resistant Bacteria in February 2009.
- Duke News also reported on the Donald Lab's work in enzyme design in the February 2009 article Duke Software Dramatically Speeds Enzyme Design.
- Congratulations to Chittu
and his wife Julie on the birth of their daughter,
Chijul Bruce Tripathy, on August 4, 2008! Chijul's
middle name is named after Chittu's Ph.D. advisor, Bruce Randall Donald, whose
middle name is after Bruce's father's advisor, James G. Randall.
- Duke team creates a fleet of crawling robots, a News & Observer article about the Donald Lab constructing a fleet of fully steerable microrobots appeared in June 2008.
- Microrobotic Ballet, A Duke News article and video about the Donald Lab's microscopic robots maneuvering independently on a stage one millimeter square appeared in June 2008.
- Nicholas Patrick, a junior majoring in Computer Science and a member of the Donald Lab, is one of three Duke students selected for a Goldwater Scholarship in science, mathematics and engineering for the 2008-09 academic year. More »
- An article on the Donald Lab's work in computational redesign of nature's molecular assembly lines appeared in the Spring 2008 issue of Duke's Department of Computer Science newsletter, Threads.
- While numerous inhibitors of enzymatic activity have been
developed, the development of inhibitors of protein-protein
interactions has only recently come to the forefront as a viable
approach. Allosteric inhibition of such protein-protein interactions
presents a number of advantages, including not having to compete for
binding with the partner protein. However, to date there are very few
examples of such inhibitors. We have developed novel allosteric
small-molecule inhibitors of the binding of RUNX1 to CBFβ, two proteins whose translocations play a
critical role in the development of acute myeloid leukemia and acute
lymphocytic leukemia. The results are reported in the cover
article of Chemistry
& Biology, (Cell Press, 2007) [More »].
- Two of our papers on protein design were recommended reading "of
outstanding interest" by
SM Lippow & B Tidor. Progress in computational protein design.
Curr Opin Biotechnol. 2007 Jul 17; Medline.
- Bruce Donald gave the Inaugural Lecture, for
Nanotechnology Public Lecture Series on April 19, 2007. (Announcement)
View the lecture.
articles about the Donald Lab (1993-2006)