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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)
We present results of phase shift for I = 2 S-wave ππ system with the Wilson fermions in the quenched approximation. The finite size method proposed by Lüscher is employed, and calculations are carried out at
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)
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)
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)
We present our final results of the charmonium spectrum in quenched QCD on anisotropic lattices. Simulations are made with the plaquette gauge action and a tadpole improved clover quark action employing ξ = as/at = 3. We calculate the spectrum of Sand P-states and their excitation, and study the scaling behavior of mass splittings. Comparison is made with… (More)
We present a fully non-perturbative determination of the O(a) improvement coefficient cSW in three-flavor dynamical QCD for the RG improved as well as the plaquette gauge actions, using the Schrödinger functional scheme. Results are compared with one-loop estimates at weak gauge coupling.
We present a calculation of the scattering phase shift for the I = 2 S-wave pion-pion system in the continuum limit with two-flavor full QCD. Calculations are made at three lattice spacings, using the finite volume method of Lüscher in the center of mass frame, and its extension to the laboratory frame.
We explore the region of small sea quark masses below mP S /mV = 0.5 in two-flavor QCD using a mean-field improved clover quark action and an RG-improved gauge action at a ≃ 0.2 fm on 12 3 × 24 and 16 3 × 24 lattices. We find that instability of the standard BiCGStab algorithm at small quark masses can be mostly removed by the BiCGStab(DS-L) algorithm,… (More)