A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots

This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal pseudoknot-free structure are likely to be part of the true structure. Thus seeding the genetic algorithm with optimal pseudoknot-free structures will more likely lead it to the true structure than a randomly generated population. The genetic algorithm uses the known energy models with an additional augmentation to allow complex pseudoknots. The nearest-neighbor energy model is used in conjunction with Turner’s thermodynamic parameters for pseudoknot-free structures, and the H-type pseudoknot energy estimation for simple pseudoknots. Testing with known pseudoknot sequences from PseudoBase shows that it out performs some of the current popular algorithms

Selection of earthquake ground motions for multiple objectives using genetic algorithms

Existing earthquake ground motion (GM) selection methods for the seismic assessment of structural systems focus on spectral compatibility in terms of either only central values or both central values and variability. In this way, important selection criteria related to the seismology of the region, local soil conditions, strong GM intensity and duration as well as the magnitude of scale factors are considered only indirectly by setting them as constraints in the pre-processing phase in the form of permissible ranges. In this study, a novel framework for the optimum selection of earthquake GMs is presented, where the aforementioned criteria are treated explicitly as selection objectives. The framework is based on the principles of multi-objective optimization that is addressed with the aid of the Weighted Sum Method, which supports decision making both in the pre-processing and post-processing phase of the GM selection procedure. The solution of the derived equivalent single-objective optimization problem is performed by the application of a mixed-integer Genetic Algorithm and the effects of its parameters on the efficiency of the selection procedure are investigated. Application of the proposed framework shows that it is able to track GM sets that not only provide excellent spectral matching but they are also able to simultaneously consider more explicitly a set of additional criteria

Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

A rewriting grammar for heat exchanger network structure evolution with stream splitting

The design of cost optimal heat exchanger networks is a difficult optimisation problem due both to the nonlinear models required and also the combinatorial size of the search space. When stream splitting is considered, the combinatorial aspects make the problem even harder. This paper describes the implementation of a two level evolutionary algorithm based on a string rewriting grammar for the evolution of the heat exchanger network structure. A biological analogue of genotypes and phenotypes is used to describe structures and specific solutions respectively. The top level algorithm evolves structures while the lower level optimises specific structures. The result is a hybrid optimisation procedure which can identify the best structures including stream splitting. Case studies from the literature are presented to demonstrate the capabilities of the novel procedure

Chemical structure matching using correlation matrix memories

This paper describes the application of the Relaxation By Elimination (RBE) method to matching the 3D structure of molecules in chemical databases within the frame work of binary correlation matrix memories. The paper illustrates that, when combined with distributed representations, the method maps well onto these networks, allowing high performance implementation in parallel systems. It outlines the motivation, the neural architecture, the RBE method and presents some results of matching small molecules against a database of 100,000 models