Vikram K. Mulligan

Data visualization of an influenza binder. Coral-like orange and blue organic structures over a light orange background.
Vikram K. Mulligan 
Influenza Binder, 2015
80 Million Core-Hours
This image shows the surface of an influenza virus. Influenza binds to and enters host cells using a protein on its surface called influenza hemagglutinin, which is the large, bulbous brown structure that occupies much of the field of view. In blue is an artificial protein that was designed to bind to the lower “stem” region of hemagglutinin, and to prevent the molecular motions that it must undergo in order to allow the virus to fuse with a host cell. This protein was designed by Sarel Fleichman, Eva Strauch, and others in the Institute for Protein Design at the University of Washington. It is hoped that proteins like these could one day be useful for preventing or treating influenza infection.
Data visualization of a Peptide Drug Concept. Molecular mass in blue, red, white, yellow, and orange colors. Centrally floating on a smoky light-blue background.
Vikram K. Mulligan 
Peptide Drug Concept, 2014
200 Million Core-Hours
Peptides offer enormous potential as drugs. Computational methods developed in the last ten years permit us to design peptides which can be chemically synthesized from mixtures of natural and artificial amino acid building-blocks, and which fold into conformations that are shaped perfectly to bind to pockets in target proteins. If the target protein is involved in human disease, and if the binding interferes with the function of that protein in some way, the peptide can potentially be used to treat that disease. Here, an early design for an anti-HIV peptide is shown in gold, bound to an HIV protein that the peptide is intended to inhibit. 
Data visualization of a Peptide Folding Landscape. Small molecular masses scattered over a hilly internal landscape. A spotlight from the top illuminates the hills and masses with an orange glow, surrounded by blackness.
Vikram K. Mulligan 
The Peptide Folding Landscape, 2018
120 Million Core-Hours
Peptides are small chains of amino acids, and like their longer cousins, proteins, they can fold into well-defined three-dimensional structures. This illustration is meant to represent the concept of a folding free-energy landscape, which is an arrangement of the many different conformations that a peptide can adopt in space, in which similar conformations are placed close to one another. In this conceptual view, the energy of each conformational state is represented as the height of that point in the landscape, with the folded state occupying the lowest point in the landscape since it is the most stable conformation (i.e. the conformation with the lowest energy). Where the number of conformations that any given protein can adopt is astronomical, small peptides (and particularly peptide macrocycles, which have their ends joined) are much more constrained, and recently-developed computational methods allow exhaustive or near-exhaustive exploration of the accessible conformations to predict the lowest-energy state. This illustration was made following the acceptance of Hosseinzadeh, Bhardwaj, Mulligan et al. (2017) Science 358(6369):1461-6 for publication, a paper in which we presented new computational methods for designing peptides that fold and predicting how peptides fold. 
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