Victor I. Lesk

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~CP-PACS Collaboration! Institute of Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan Center for Computational Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Institute for Cosmic Ray Research, University of Tokyo, Kashiwa 277-8582, Japan High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan(More)
We present a lattice QCD calculation of the scattering phase shift for the I = 2 S-wave two-pion system using the finite size method proposed by Lüscher. We work in the quenched approximation employing the standard plaquette action at β = 5.9 for gluons and the Wilson fermion action for quarks. The phase shift is extracted from the energy eigenvalues of the(More)
Understanding protein interactions has broad implications for the mechanism of recognition, protein design, and assigning putative functions to uncharacterized proteins. Studying protein flexibility is a key component in the challenge of describing protein interactions. In this work, we characterize the observed conformational change for a set of 20(More)
In rounds 3-5 of CAPRI, the community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction, we applied the 3D-Dock software package to predict the atomic structures of nine biophysical interactions. This approach starts with an initial grid-based shape complementarity search. The product of this is a large number(More)
MOTIVATION Reliable structural modelling of protein-protein complexes has widespread application, from drug design to advancing our knowledge of protein interactions and function. This work addresses three important issues in protein-protein docking: implementing backbone flexibility, incorporating prior indications from experiment and bioinformatics, and(More)
Bacteria produce an array of glycan-based structures including capsules, lipo-oligosaccharide and glycosylated proteins, which are invariably cell-surface-located. For pathogenic bacteria, such structures are involved in diverse roles in the life cycle of the bacterium, including adhesion, colonization, avoidance of predation and interactions with the(More)
Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two(More)
~CP-PACS Collaboration! Institute of Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan Center for Computational Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Institute for Cosmic Ray Research, University of Tokyo, Kashiwa 277-8582, Japan High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan(More)
The National Biomedical Research Foundation-Protein Identification Resource (NBRF-PIR) and the Protein Data Bank at Brookhaven National Laboratory (PDB) both contain protein sequences. We have prepared a cross-reference index of the sequences in these data banks, and compared the data. Of the 270 cases of sequences of the same protein appearing in both data(More)
N. Tsutsui, c A. Ukawa, a,d T. Umeda, N. Yamada and T. Yoshié Institute of Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan Institute for Cosmic Ray Research, University of Tokyo, Kashiwa, Chiba 277-8582, Japan High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan Center for Computational Physics, University(More)