of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F²Dock (F² = Fast Fourier). We have calibrated F²Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F²Dock works very well in practice. Though

It is well known that the prolonged use of current HIV drugs leads to drug-resistance and mutation. Therefore, the development of new HIV protease inhibitors that are active against mutant viruses is highly desirable. The shape and electrostatic complementarity has been recognized as one of the key

ABSTRACT We present a new computational method of docking pairs of proteins by using spherical polar Fourier correlations to accelerate the search for candidate low-energy conformations. Interaction energies are estimated using a hydrophobic excluded volume model derived from the notion

alignment of the two 3D protein surface patches. Compared with the fast Fourier transform-based global geometric matching algorithm and other methods, our FlexDock system generates much less false-positive docking results, which benefits identification of the complementary candidates. Our computational

of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction

the potential repertoires are described by the genomic T cell receptor (TR) and immunoglobulin (IG) loci. TR and IG are produced by random somatic rearrangements of V, D, and J genes during lymphocyte differentiation. The product of the V-(D)-J joining, called the complementarity determining region 3 (CDR3

The principle aim of this dissertation is to investigate the philosophical application of quantum information theory to interpretational issues regarding the theory of quantum mechanics. Recently, quantum information theory has emerged as a potential source for such an interpretation. The main question with which this dissertation will be concerned is whether or not an information-theoretic interpretation can serve as a conceptually acceptable interpretation of quantum mechanics. It will be argued that some of the more obvious approaches – that quantum information theory shows us that ultimately the world is made of information, and quantum Bayesianism – fail as philosophical interpretations of quantum mechanics. However, the information-theoretic approach of Clifton, Bub, and Halvorson introduces Einstein’s distinction between principle theories and constructive theories, arguing that quantum mechanics is best understood as an information-theoretic principle theory. While I argue that this particular approach fails, it does offer a viable new philosophical role for information theory. Specifically, an investigation of interpretationally successful principle theories such as Newtonian mechanics, special relativity, and general