Ryan H. Lilien

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We have developed an algorithm called Q5 for probabilistic classification of healthy versus disease whole serum samples using mass spectrometry. The algorithm employs principal components analysis (PCA) followed by linear discriminant analysis (LDA) on whole spectrum surface-enhanced laser desorption/ionization time of flight (SELDI-TOF) mass spectrometry(More)
One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign(More)
High-throughput NMR structural biology can play an important role in structural genomics. We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. These assignments are a prerequisite for probing protein-protein interactions, protein-ligand binding, and dynamics by NMR.(More)
Realization of novel molecular function requires the ability to alter molecular complex formation. Enzymatic function can be altered by changing enzyme-substrate interactions via modification of an enzyme's active site. A redesigned enzyme may either perform a novel reaction on its native substrates or its native reaction on novel substrates. A number of(More)
UNLABELLED We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations(More)
MOTIVATION Structure-based protein redesign can help engineer proteins with desired novel function. Improving computational efficiency while still maintaining the accuracy of the design predictions has been a major goal for protein design algorithms. The combinatorial nature of protein design results both from allowing residue mutations and from the(More)
Michael J. Gorczynski,1,7 Jolanta Grembecka,2 Yunpeng Zhou,2 Yali Kong,3 Liya Roudaia,4 Michael G. Douvas,5 Miki Newman,2 Izabela Bielnicka,2 Gwen Baber,2 Takeshi Corpora,2 Jianxia Shi,2,8 Mohini Sridharan,6 Ryan Lilien,6 Bruce R. Donald,6,9 Nancy A. Speck,4 Milton L. Brown,3,* and John H. Bushweller2,* 1Department of Chemistry, University of Virginia,(More)
In this paper, we discuss the adaptation of an open-source single-user, single-display molecular visualization application for use in a multi-display, multi-user environment. Jmol, a popular, open-source Java applet for viewing PDB files, is modified in such a manner that allows synchronized coordinated views of the same molecule to be displayed in a(More)
We have developed an algorithm called Q5 for probabilistic classiŽ cation of healthy versus disease whole serum samples using mass spectrometry. The algorithm employs principal components analysis (PCA) followed by linear discriminant analysis (LDA) on whole spectrum surface-enhanced laser desorption/ionization time of  ight (SELDI-TOF) mass spectrometry(More)
We have determined the crystal structure of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis, revealing a unique linker domain containing an 11-residue alpha-helix that has extensive interactions with the opposite DHFR-TS monomer of the homodimeric enzyme. Analysis of the structure of DHFR-TS from C. hominis and of(More)