Results 1  10
of
16
Constraint logic programming approach to protein structure prediction
 BMC Bioinformatics
, 2004
"... Background The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization prob ..."
Abstract

Cited by 35 (16 self)
 Add to MetaCart
(Show Context)
Background The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Results Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the facecentered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the facecentered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a wellestablished technique as molecular dynamics. Conclusions The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The
Replication and Mutation on Neutral Networks
, 2000
"... Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely de ned base pairing pattern to every sequence. The mapping is noninvertible since many sequences fold into the same minimum free energy (secondary) structure or shape. The preimages of this map, called ne ..."
Abstract

Cited by 32 (9 self)
 Add to MetaCart
Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely de ned base pairing pattern to every sequence. The mapping is noninvertible since many sequences fold into the same minimum free energy (secondary) structure or shape. The preimages of this map, called neutral networks, are uniquely associated with the shapes and vice versa. Random graph theory is used to construct networks in sequence space which are suitable models for neutral networks. The theory of molecular quasispecies has been applied to replication and mutation on singlepeak tness landscapes. This concept is extended by considering evolution on degenerate multipeak landscapes which originate from neutral networks by assuming that one particular shape is tter than all others. On such a singleshape landscape the superior tness value is assigned to all sequences belonging
Molecular Insights into Evolution of Phenotypes
, 2000
"... re analyzed for RNA secondary structures. Optimization of molecular properties in populations is modeled in silico through replication and mutation in a flow reactor. The approach towards a predefined structure is monitored and reconstructed in terms of an uninterrupted series of phenotypes from ..."
Abstract

Cited by 21 (9 self)
 Add to MetaCart
re analyzed for RNA secondary structures. Optimization of molecular properties in populations is modeled in silico through replication and mutation in a flow reactor. The approach towards a predefined structure is monitored and reconstructed in terms of an uninterrupted series of phenotypes from initial stucture to target, called relay series. We give a novel definition of continuity in evolution which identifies discontinuities as major changes in molecular phenotypes. Evolutionary Dynamics  Exploring the Interplay of Accident, Selection, Neutrality, and Function Edited by J. P. Crutchfield and P. Schuster, Oxford Univ. Press 1 2 Evolution of Phenotypes 1 GENOTYPES AND PHENOTYPES Evolutionary optimization in asexually multiplying populations follows Darwin 's principle and is determined by the interplay of two processes which exert counteracting influences on genetic heterogeneity: (i) Mutations increase di
Landscapes and Effective Fitness
, 2003
"... The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged as useful conceptual tools with which to understand the dynamics of evolutionary processes, especially in the presence of complex genotypeph ..."
Abstract

Cited by 12 (2 self)
 Add to MetaCart
(Show Context)
The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged as useful conceptual tools with which to understand the dynamics of evolutionary processes, especially in the presence of complex genotypephenotype relations. In this contribution we attempt to provide a unified discussion of these two approaches, discussing both their advantages and disadvantages in the context of some simple models. We also discuss how fitness and effective fitness change under various transformations of the configuration space of the underlying genetic model, concentrating on coarse graining transformations and on a particular coordinate transformation that provides an appropriate basis for illuminating the structure and consequences of recombination.
Evolution in silico and in vitro: The RNA model
"... Theoretical concepts and experiments dealing with evolution of molecules in vitro reached a state that allows for direct applications to the design of biomolecules with predefined properties. RNA evolution in vitro represents a basis for the development of a new and comprehensive model of evolution ..."
Abstract

Cited by 11 (3 self)
 Add to MetaCart
Theoretical concepts and experiments dealing with evolution of molecules in vitro reached a state that allows for direct applications to the design of biomolecules with predefined properties. RNA evolution in vitro represents a basis for the development of a new and comprehensive model of evolution focusing on the phenotype and its fitness relevant properties. Relations between genotypes and phenotypes are described by mappings from genotype space onto a space of phenotypes, which are manytoone and thus give ample room for neutrality as expressed by existence of extended neutral networks in genotype space. The RNA model reduces genotypephenotype relations to mappings from sequences into secondary structures of minimal free energies and allows for derivation of otherwise inaccessible quantitative results. Continuity and discontinuity in evolution are defined through a new notion of accessibility in phenotype space that provides a basis for straightforward interpretation of computer simulations on RNA optimization and reveal the constructive role of random genomic drift in the search for phenotypes of higher fitness. The effects of population size on the course of evolutionary optimization can be predicted quantitatively by means of a simple stochastic model based on a birthanddeath process with immigration.
NEUTRAL NETWORKS OF SEQUENCE TO SHAPE MAPS
, 2007
"... In this paper we present a novel framework for sequence to shape maps. These combinatorial maps realize exponentially many shapes, and have preimages which contain extended connected subgraphs of diameter n (neutral networks). We prove that all basic properties of RNA folding maps also hold for com ..."
Abstract
 Add to MetaCart
(Show Context)
In this paper we present a novel framework for sequence to shape maps. These combinatorial maps realize exponentially many shapes, and have preimages which contain extended connected subgraphs of diameter n (neutral networks). We prove that all basic properties of RNA folding maps also hold for combinatorial maps. Our construction is as follows: suppose we are given a graph H over the {1..., n} and an alphabet of nucleotides together with a symmetric relation R, implied by base pairing rules. Then the shape of a sequence of length n is the maximal H subgraph in which all pairs of nucleotides incident to Hedges satisfy R. Our main result is to prove the existence of at least √ 2 n−1 shapes with extended neutral networks, i.e. shapes that have a preimage with diameter n and a connected component of size at least ( 1+√5) 2 n + ( 1−√5) 2 n. Furthermore, we show that there exists a certain subset of shapes which carries a natural graph structure. In this graph any two shapes are connected by a path of shapes with respective neutral networks of distance one. We finally discuss our results and provide a comparison with RNA folding maps.
common volumes
, 2004
"... Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of ..."
Abstract
 Add to MetaCart
(Show Context)
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of