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  • Oral presentation
  • Open Access

Targeting protein dynamics in drug design

Journal of Cheminformatics20135 (Suppl 1) :O1

  • Published:


  • Target Protein
  • Dynamic Nature
  • Drug Design
  • Protein Dynamic
  • Ligand Design

The dynamic nature of protein structures provides challenges and opportunities for ligand design. I will first discuss some of the different ways in which protein dynamics can be targeted, giving examples from our experience in the design of inhibitors of thymidylate synthase [13]. I will then describe the development of a computational toolbox (TRAPP: TRAnsient Pockets in Proteins) to identify and visualize transient pockets in proteins that may be exploited in ligand design.

Authors’ Affiliations

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Germany
Center for Molecular Biology (ZMBH), Heidelberg University, Heidelberg, Germany


  1. Ferrari S, Costi MP, Wade RC: Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase. Chem & Biol. 2003, 10: 1183-1193. 10.1016/j.chembiol.2003.11.012.View ArticleGoogle Scholar
  2. Salo-Ahen OMH, Wade RC: The Active-Inactive Transition of Human Thymidylate Synthase: Targeted Molecular Dynamics Simulations. Proteins: Struct, Funct, Bioinf. 2011, 79: 2886-2899. 10.1002/prot.23123.View ArticleGoogle Scholar
  3. Cardinale D, Guaitolia G, Tondi D, Luciani R, Henrich S, Salo-Ahen OMH, Ferrari S, Marverti G, Guerrieri D, Ligabue A, Frassineti C, Pozzi C, Mangani S, Fessas D, Guerrini R, Ponterini G, Wade R, Costi MP: Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase. Proc Natl Acad Sci USA. 2011, 108: 13889-13890. E542-E549View ArticleGoogle Scholar


© Wade; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.