Application of Inductive Logic Programming to Discover Rules Governing the Three-Dimensional Topology of Protein Structure
نویسندگان
چکیده
Inductive Logic Programming (ILP) has been applied to discover rules governing the three-dimensional topology of protein structure. The data-set unifies two sources of information; SCOP and PROMOTIF. Cross-validation results for experiments using two background knowledge sets, global (attribute-valued) and constitutional (relational), are presented. The application makes use of a new feature of Progol4.4 for numeric parameter estimation. At this early stage of development, the rules produced can only be applied to proteins for which the secondary structure is known. However, since the rules are insightful, they should prove to be helpful in assisting the development of taxonomic schemes. The application of ILP to fold recognition represents a novel and promising approach to this problem.
منابع مشابه
Application of machine learning to structural molecular biology.
A technique of machine learning, inductive logic programming implemented in the program GOLEM, has been applied to three problems in structural molecular biology. These problems are: the prediction of protein secondary structure; the identification of rules governing the arrangement of beta-sheets strands in the tertiary folding of proteins; and the modelling of a quantitative structure activit...
متن کاملUse of Inductive Logic Programming to Learn Principles of Protein Structure
Inductive Logic Programming (ILP) has been applied to learn rules which characterise protein folds. Several representations for the background set have been explored and the results have been interpreted in their biological context. In this paper, we present new results obtained with a background set containing information about protein topology. The new rules are more descriptive than the prev...
متن کاملInductive Logic Programming Used to Discover Topological Constraints in Protein Structures
This paper describes the application of the Inductive Logic Programming (ILP) program GOLEM to the discovery of constraints in the packing of beta-sheets in alpha/beta proteins. These constraints (rules) have a role in understanding the protein folding problem. Constraints were learnt for four features of beta-sheet packing: the winding direction of two sequential strands, whether two consecuti...
متن کاملDAMAGE IDENTIFICATION BY USING MODAL EXPANSION AND TOPOLOGY OPTIMIZATION IN THREE DIMENSIONAL ELASTICITY PROBLEMS
In this paper, topology optimization is utilized for damage detection in three dimensional elasticity problems. In addition, two mode expansion techniques are used to derive unknown modal data from measured data identified by installed sensors. Damages in the model are assumed as reduction of mass and stiffness in the discretized finite elements. The Solid Isotropic Material with Penalization (...
متن کاملAutomated identification of features of protein-ligand interactions using inductive logic programming: application to hexose binding
Motivation: There is an urgent need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP) which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity requi...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 1998