Jerry W. Tsai

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Template based protein structure prediction (commonly referred to as homology or comparative modeling) uses knowledge of solved structures to model a protein sequence's native or true fold. First, a parent structure is found and then a template structure is built by mapping the target sequence onto the parent structure. This putative structure is refined(More)
The tremendous therapeutic potential of peptides has not yet been realized, mainly owing to their short in vivo half-life. Although conjugation to macromolecules has been a mainstay approach for enhancing protein half-life, the steric hindrance of macromolecules often harms the binding of peptides to target receptors, compromising the in vivo efficacy. Here(More)
Interest in predicting protein backbone conformational angles has prompted the development of modeling and inference procedures for bivariate angular distributions. We present a Bayesian approach to density estimation for bivariate angular data that uses a Dirichlet process mixture model and a bivariate von Mises distribution. We derive the necessary full(More)
MOTIVATION While protein secondary structure is well understood, representing the repetitive nature of tertiary packing in proteins remains difficult. We have developed a construct called the relative packing group (RPG) that applies the clique concept from graph theory as a natural basis for defining the packing motifs in proteins. An RPG is defined as a(More)
Determining the primary structure (i.e., amino acid sequence) of a protein has become cheaper, faster, and more accurate. Higher order protein structure provides insight into a protein's function in the cell. Understanding a protein's secondary structure is a first step towards this goal. Therefore, a number of computational prediction methods have been(More)
The methylotrophic yeast, Pichia pastoris, has been genetically engineered to produce many heterologous proteins for industrial and research purposes. In order to secrete proteins for easier purification from the extracellular medium, the coding sequence of recombinant proteins is initially fused to the Saccharomyces cerevisiae α-mating factor secretion(More)
By providing new insights into the distribution of a protein's torsion angles, recent statistical models for this data have pointed the way to more efficient methods for protein structure prediction. Most current approaches have concentrated on bivariate models at a single sequence position. There is, however, considerable value in simultaneously modeling(More)
Grouping the 20 residues is a classic strategy to discover ordered patterns and insights about the fundamental nature of proteins, their structure, and how they fold. Usually, this categorization is based on the biophysical and/or structural properties of a residue's side-chain group. We extend this approach to understand the effects of side chains on(More)
In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome(More)
Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages(More)