The InterCriteria Analysis Portal

Active projects

Project title

DN17/6 2017 A New Approach, Based on an Intercriteria Data Analysis, to Support Decision Making in in silico Studies of Complex Biomolecular Systems

The proposed project aims at developing a new approach to supporting the decision making process in in silico studies of complex biomolecular systems using intercriteria analysis (ICrA). Molecular, and in particular drug design, is a time-consuming and costly process that motivates intensive development and use of computer-aided (in-silico) approaches. These approaches are strongly interdisciplinary and integrate knowledge from basic disciplines such as chemistry, biology, physics, pharmacology, toxicology, mathematical modeling, and informatics. A key element in the algorithms for docking and virtual screening of bioactive molecules is the scoring function, the purpose of which is to quickly and accurately calculate the energy of the interaction of the protein ligand complex. Despite the large number of comparative studies of various scoring functions, the question of which docking programs and protocols are performing better is still unresolved and the results are often contradictory. ICrA, developed as a new multi-criterion decision-making approach, has the necessary prerequisites to assist in choosing the most appropriate scoring functions in order to guide the selection of the most appropriate drug candidates. The proposed project aims to conduct theoretical research, combining ICrA-based techniques of artificial intelligence (intuitionistic fuzzy logic and indexed matrices) and in silico methods for molecular design.
The working hypothesis of the project is based on the assumption that inter-criteria analysis can support decision-making in structure-based in silico studies of complex biomolecular systems, offering a new approach to assessing the results of using different scoring functions in docking protocols. The hypothesis will be proved by fulfilling the following main objectives:
1. To investigate the applicability of ICrA to scoring functions of different types and from different software implementations for molecular modelling (commercial and free) on a set of experimental data on structures and activities of various protein-ligand complexes.
2. To investigate the applicability of ICrA with respect to different indicators (interaction energies and binding poses) for evaluation of the results of docking and post-dock optimization of protein-ligand complexes.
3. Based on objectives 1 and 2, to develop a prototype of a software environment, implementing the ICrA capabilities.
4. Based on objectives 1, 2 and 3, to estimate the potential of ICrA to assist decision making in in silico studies of complex biomolecular systems, and to stimulate its further development
The results obtained for evaluation, comparison and selection of molecular dock assessment functions are expected to support decision making in in silico molecular design and be useful for researchers in choosing the most appropriate compounds for drug candidates.

Completed projects

Project title

DFNI-I-02-5 “InterCriteria Analysis – A New Approach to Decision Making”

Project annotation

Our goal is to develop a new approach of decision making support, recently defined by the project team and named by us InterCriteria Analysis. Under this approach, arrays of data obtained by the measurement of many objects against many criteria are processed until correlations are calculated for each pair of criteria in the form of intuitionistic fuzzy pairs of values in the [0;1]-interval. The approach renders account of uncertainty, allows processing of arrays with missing data, and handles both numerical data and linguistic variables with introduced ordering.

The InterCriteria Analysis can be successfully applied to problems, where measuring according to some of the criteria is slower or more expensive, which results in delaying or raising the cost of the overall process of decision making. When solving such problems it is necessary to adopt an approach for reasonable elimination of these criteria, in order to achieve economy and efficiency.

The approach has already demonstrated first evidences of its potential, when applied to economic data, and there have been outlined specific areas of its future application, for which we can obtain appropriate test data. Hence, one of the project objectives is specifying the general framework of the problems addressed by the approach. There will be investigated the connections between the new approach and the multicriteria decision making methods, as well as its relation with the cognitive maps. Another project objective is the development of a software application, implementing the InterCriteria Analysis approach.

Used methods: The approach is based on two mathematical formalisms, which are also original developments of the project team: 1. The algebraic apparatus of index matrices for processing of data arrays of diverse dimensions, and 2. The intuitionistic fuzzy sets as a mathematical tool for treating uncertainty.

Expected results: A new approach will be elaborated in details for solving a class of problems that often occur in science, medicine and industry, and have an important economic and social effect. The approach will be provided with a software application, and approbated with real data from fields of medicine, ecology, agriculture, economics, industry, and artificial intelligence.

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