This article is part of the supplement: Proceedings of the 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-meeting 2009)

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Mining flexible-receptor docking experiments to select promising protein receptor snapshots

Karina S Machado1, Ana T Winck2, Duncan DA Ruiz2 and Osmar Norberto de Souza1*

Author Affiliations

1 LABIO - Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas. PPGCC, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681 – Prédio 32, sala 602, 90619-900, Porto Alegre, RS, Brazil

2 GPIN - Grupo de Pesquisa em Inteligência de Negócio. PPGCC, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681 – Prédio 32, sala 628, 90619-900, Porto Alegre, RS, Brazil

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BMC Genomics 2010, 11(Suppl 5):S6  doi:10.1186/1471-2164-11-S5-S6

Published: 22 December 2010



Molecular docking simulation is the Rational Drug Design (RDD) step that investigates the affinity between protein receptors and ligands. Typically, molecular docking algorithms consider receptors as rigid bodies. Receptors are, however, intrinsically flexible in the cellular environment. The use of a time series of receptor conformations is an approach to explore its flexibility in molecular docking computer simulations, but it is extensively time-consuming. Hence, selection of the most promising conformations can accelerate docking experiments and, consequently, the RDD efforts.


We previously docked four ligands (NADH, TCL, PIF and ETH) to 3,100 conformations of the InhA receptor from M. tuberculosis. Based on the receptor residues-ligand distances we preprocessed all docking results to generate appropriate input to mine data. Data preprocessing was done by calculating the shortest interatomic distances between the ligand and the receptor’s residues for each docking result. They were the predictive attributes. The target attribute was the estimated free-energy of binding (FEB) value calculated by the AutodDock3.0.5 software. The mining inputs were submitted to the M5P model tree algorithm. It resulted in short and understandable trees. On the basis of the correlation values, for NADH, TCL and PIF we obtained more than 95% correlation while for ETH, only about 60%. Post processing the generated model trees for each of its linear models (LMs), we calculated the average FEB for their associated instances. From these values we considered a LM as representative if its average FEB was smaller than or equal the average FEB of the test set. The instances in the selected LMs were considered the most promising snapshots. It totalized 1,521, 1,780, 2,085 and 902 snapshots, for NADH, TCL, PIF and ETH respectively.


By post processing the generated model trees we were able to propose a criterion of selection of linear models which, in turn, is capable of selecting a set of promising receptor conformations. As future work we intend to go further and use these results to elaborate a strategy to preprocess the receptors 3-D spatial conformation in order to predict FEB values. Besides, we intend to select other compounds, among the million catalogued, that may be promising as new drug candidates for our particular protein receptor target.