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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)
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)
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)
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)