A ligand predication tool based on modeling and reasoning with imprecise probabilistic knowledge

  • Authors:

  • Weiru Liu;Anbu Yue;David J. Timson

  • Affiliations:

  • School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast BT7 1NN, UK;School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast BT7 1NN, UK;School of Biological Science, Queen's University Belfast, Belfast BT9 7BL, UK

  • Venue:
  • Computer Methods and Programs in Biomedicine
  • Year:
  • 2010

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Abstract

Ligand prediction has been driven by a fundamental desire to understand more about how biomolecules recognize their ligands and by the commercial imperative to develop new drugs. Most of the current available software systems are very complex and time-consuming to use. Therefore, developing simple and efficient tools to perform initial screening of interesting compounds is an appealing idea. In this paper, we introduce our tool for very rapid screening for likely ligands (either substrates or inhibitors) based on reasoning with imprecise probabilistic knowledge elicited from past experiments. Probabilistic knowledge is input to the system via a user-friendly interface showing a base compound structure. A prediction of whether a particular compound is a substrate is queried against the acquired probabilistic knowledge base and a probability is returned as an indication of the prediction. This tool will be particularly useful in situations where a number of similar compounds have been screened experimentally, but information is not available for all possible members of that group of compounds. We use two case studies to demonstrate how to use the tool.