Annals of Operations Research - Special issue on Tabu search
A molecular structure matching problem
Computers and Operations Research
Computers and Operations Research
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Handbook of Evolutionary Computation
Handbook of Evolutionary Computation
Genetic Programming III: Darwinian Invention & Problem Solving
Genetic Programming III: Darwinian Invention & Problem Solving
The Design of Innovation: Lessons from and for Competent Genetic Algorithms
The Design of Innovation: Lessons from and for Competent Genetic Algorithms
Co-evolving Memetic Algorithms: Initial Investigations
PPSN VII Proceedings of the 7th International Conference on Parallel Problem Solving from Nature
Alignment Of Protein Structures With A Memetic Evolutionary Algorithm
GECCO '02 Proceedings of the Genetic and Evolutionary Computation Conference
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Ant colony system: a cooperative learning approach to the traveling salesman problem
IEEE Transactions on Evolutionary Computation
No free lunch theorems for optimization
IEEE Transactions on Evolutionary Computation
A Study on the use of "self-generation'' in memetic algorithms
Natural Computing: an international journal
Credit assignment in adaptive memetic algorithms
Proceedings of the 9th annual conference on Genetic and evolutionary computation
An unorthodox introduction to Memetic Algorithms
ACM SIGEVOlution
Bimal: bipartite matching alignment for the contact map overlap problem
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
A fuzzy sets based generalization of contact maps for the overlap of protein structures
Fuzzy Sets and Systems
Joining softassign and dynamic programming for the contact map overlap problem
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Abstract functions and lifetime learning in genetic programming for symbolic regression
Proceedings of the 12th annual conference on Genetic and evolutionary computation
Using memory and fuzzy rules in a co-operative multi-thread strategy for optimization
Information Sciences: an International Journal
Estimating meme fitness in adaptive memetic algorithms for combinatorial problems
Evolutionary Computation
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In this paper we describe the application of a so called "Self-Generating" Memetic Algorithm to the Maximum Contact Map Overlap problem (MAX-CMO). The maximum overlap of contact maps is emerging as a leading modeling technique to obtain structural alignment among pairs of protein structures. Identifying structural alignments (and hence similarity among proteins) is essential to the correct assessment of the relation between proteins structure and function. A robust methodology for structural comparison could have impact on the process of rational drug design.The Self-Generating Memetic Algorithm we present in this work evolves concurrently both the solutions (i.e. proteins alignments) and the local search move operators that it needs to solve the problem instance at hand. The concurrent generation of local search strategies and solutions allows the Memetic Algorithm to produce better results than those given by a Genetic Algorithm and a Memetic Algorithm with human-designed local searchers. The approach has been tried in four different data sets (1 data set composed of randomly generated proteins and the other 3 data sets with real world proteins) with encouraging results.