Treffer: Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets

Title:
Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets
Authors:
BACKOFEN, R, WILL, S, BORNBERG-BAUER, E
Source:
Selection of papers presented at the German Conference on Bioinformatics (GCB'98, Cologne, Germany, October 1998Bioinformatics (Oxford. Print). 15(3):234-242
Publisher Information:
Oxford: Oxford University Press, 1999.
Publication Year:
1999
Physical Description:
print, 30 ref
Original Material:
INIST-CNRS
Subject Terms:
Bioinformatics, Bioinformatique, Sciences biologiques et medicales, Biological and medical sciences, Sciences biologiques fondamentales et appliquees. Psychologie, Fundamental and applied biological sciences. Psychology, Generalites, General aspects, Mathématiques biologiques. Statistiques. Modèles. Métrologie. Informatique en biologie (généralités), Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects), Traitement informatique, Computerized processing, Tratamiento informático, Analyse structurale, Structural analysis, Análisis estructural, Hydrophobicité, Hydrophobicity, Hidrofobicidad, Modèle réticulaire, Lattice model, Modelo reticular, Modélisation, Modeling, Modelización, Méthode, Method, Método, Polarité, Polarity, Polaridad, Programmation logique avec contrainte, Constraint logic programming, Programación lógica con restricción, Protéine, Protein, Proteína, Prédiction, Prediction, Predicción, Structure réticulée, Lattice structure, Estructura reticulada
Document Type:
Konferenz Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Institut für Informatik, LMU Munchen, Oettingenstrasse 67, 80538 München, Germany
Theoretical Bioinformatics Group, German Cancer Research Centre, Im Neuenheimer Feld 280, 65120 Heidelberg, Germany
ISSN:
1367-4803
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=1831992
Rights:
Copyright 1999 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Biological sciences. Generalities. Modelling. Methods

Generalities in biological sciences
Accession Number:
edscal.1831992
Database:
PASCAL Archive

Weitere Informationen

Motivation: Predicting the ground state of biopolymers is a notoriously hard problem in biocomputing. Model systems, such as lattice proteins, are simple tools and valuable to test and improve new methods. Best known are models with sequences composed from a binary (hydrophobic and polar) alphabet. The major drawback is the degeneracy, i.e. the number of different ground state conformations. Results: We show how recently developed constraint programming techniques can be used to solve the structure prediction problem efficiently for a higher order alphabet. To our knowledge it is the first report of an exact and computationally feasible solution to model proteins oflength up to 36 and without resorting to maximally compact states. We further show that degeneracy is reduced by more than one order ofmagnitude and that ground state conformations are not necessarily compact. Therefore, more realistic protein simulations become feasible with our model.