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D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman, “AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules,” Computer Physics Communications, Vol. 91, No. 1-3, pp. 1-41. doi:10.1016/0010-4655(95)00041-D

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• TITLE: BEAR, a Molecular Docking Refinement and Rescoring Method

  AUTHORS: Andrew Anighoro, Giulio Rastelli

  KEYWORDS: Virtual Screening; Bear; Structure-Based Drug Design

  JOURNAL NAME: Computational Molecular Bioscience, Vol.3 No.2, June 10, 2013

  ABSTRACT: BEAR (Binding Estimation After Refinement) is a computational method for structure-based virtual screening. It was set up as a post-docking processing tool for the refinement of ligand binding modes predicted by molecular docking programs and the accurate evaluation of free energies of binding. BEAR has been validated in a number of computational drug discovery applications. It performed well in discriminating active ligands with respect to molecular decoys of biological targets belonging to different protein families as well as in discovering biologically active hits. Recently, it has also been validated in the emerging field of G-protein coupled receptors structure based virtual screening.