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Gaussian-Based Approaches to Protein-Structure Similarity

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Molecular Modeling and Prediction of Bioactivity

Abstract

The number of protein structures available in the PDB1 (7415 in July 22, 1998) is constantly growing and it is expected to increase even more rapidly in coming years.2 This tremendous body of information is certainly having an impact in ligand design and modelling where the knowledge of the crystal structure of the target protein, or a closely related protein, makes a significant difference in the process of ligand optimization.3 When a crystal structure of the target protein is unavailable, ligand optimization must rely on indirect approaches based on the similarity between the structures of the ligands themselves.4 However, if a three-dimensional structure of the target protein is available docking methods can be applied,5 which have the potential of providing important information on the interaction between the ligand and the residues of the given receptor site.

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Author information

Authors and Affiliations

  1. Department of Molecular Design & Informatics, N.V. Organon, 5340, BH, Oss, The Netherlands

    Jordi Mestres

  2. Computer-Aided Drug Discovery, Pharmacia & Upjohn, Kalamazoo, MI, 49001, USA

    Douglas C. Rohrer & Gerald M. Maggiora

Authors
  1. Jordi Mestres
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  2. Douglas C. Rohrer
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  3. Gerald M. Maggiora
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Editor information

Editors and Affiliations

  1. H. Lundbeck A/S, Valby, Denmark

    Klaus Gundertofte

  2. Royal Danish School of Pharmacy, Copenhagen, Denmark

    Flemming Steen Jørgensen

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Mestres, J., Rohrer, D.C., Maggiora, G.M. (2000). Gaussian-Based Approaches to Protein-Structure Similarity. In: Gundertofte, K., Jørgensen, F.S. (eds) Molecular Modeling and Prediction of Bioactivity. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-4141-7_8

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  • DOI: https://doi.org/10.1007/978-1-4615-4141-7_8

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-6857-1

  • Online ISBN: 978-1-4615-4141-7

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