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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)
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 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)
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)
In designing an algorithm to find pairs of points that are within Euclidean distance d it is effective to use a screening procedure to reject most pairs of points that are far apart. A procedure based on multiple, overlapping lattices can efficiently identify close points and exclude distant ones.