15,183 research outputs found
Flexible protein folding by ant colony optimization
Protein structure prediction is one of the most challenging topics in bioinformatics.
As the protein structure is found to be closely related to its functions,
predicting the folding structure of a protein to judge its functions is meaningful to
the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving
protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice
model. Different from the previous ant algorithms for PFPs, the pheromones in the
proposed algorithm are placed on the arcs connecting adjacent squares in the lattice.
Such pheromone placement model is similar to the one used in the traveling salesmen
problems (TSPs), where pheromones are released on the arcs connecting the cities.
Moreover, the collaboration of effective heuristic and pheromone strategies greatly
enhances the performance of the algorithm so that the algorithm can achieve good
results without local search methods. By testing some benchmark two-dimensional
hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed
algorithm is quite competitive compared with some other well-known methods
for solving the same protein folding problems
Pressure-dependent 13C chemical shifts in proteins: Origins and applications
Pressure-dependent (13)C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH(3), CH(2) and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the gamma-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual (13)C alpha shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas (13)C beta shifts retain significant dependence on local compression, making them less useful as structural restraints
PT-Scotch: A tool for efficient parallel graph ordering
The parallel ordering of large graphs is a difficult problem, because on the
one hand minimum degree algorithms do not parallelize well, and on the other
hand the obtainment of high quality orderings with the nested dissection
algorithm requires efficient graph bipartitioning heuristics, the best
sequential implementations of which are also hard to parallelize. This paper
presents a set of algorithms, implemented in the PT-Scotch software package,
which allows one to order large graphs in parallel, yielding orderings the
quality of which is only slightly worse than the one of state-of-the-art
sequential algorithms. Our implementation uses the classical nested dissection
approach but relies on several novel features to solve the parallel graph
bipartitioning problem. Thanks to these improvements, PT-Scotch produces
consistently better orderings than ParMeTiS on large numbers of processors
- …