Prof. Dr. Bert L. de Groot

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  • 2020 | Journal Article | 
    ​ ​Large scale relative protein ligand binding affinities using non-equilibrium alchemy​
    Gapsys, V. ; Pérez-Benito, L.; Aldeghi, M.; Seeliger, D.; van Vlijmen, H.; Tresadern, G. & de Groot, B. L. ​ (2020) 
    Chemical Science, 11(4) pp. 1140​-1152​.​ DOI: https://doi.org/10.1039/C9SC03754C 
    ​Details  DOI 
  • 2016 | Journal Article
    ​ ​Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan​
    Gapsys, V. ; Michielssens, S.; Seeliger, D. & de Groot, B. L. ​ (2016) 
    Angewandte Chemie. International Edition, 55(26) pp. 7364​-7368​.​ DOI: https://doi.org/10.1002/anie.201510054 
    ​Details  DOI 
  • 2016 | Journal Article
    ​ ​Insights from the First Principles Based Large Scale Protein Thermostability Calculations​
    Gapsys, V. ; Michielssens, S.; Seeliger, D. & de Groot, B. L. ​ (2016) 
    Biophysical Journal, 110(3) pp. 368a​.​ DOI: https://doi.org/10.1016/j.bpj.2015.11.1985 
    ​Details  DOI 
  • 2014 | Journal Article
    ​ ​pmx: Automated protein structure and topology generation for alchemical perturbations​
    Gapsys, V.; Michielssens, S.; Seeliger, D. & de Groot, B. L. ​ (2014) 
    Journal of Computational Chemistry, 36(5) pp. 348​-354​.​ DOI: https://doi.org/10.1002/jcc.23804 
    ​Details  DOI 
  • 2014 | Journal Article | Research Paper
    ​ ​A Designed Conformational Shift To Control Protein Binding Specificity​
    Michielssens, S.; Peters, J. H.; Ban, D. ; Pratihar, S. ; Seeliger, D.; Sharma, M. & Giller, K.  et al.​ (2014) 
    Angewandte Chemie International Edition, 53(39) pp. 10367​-10371​.​ DOI: https://doi.org/10.1002/anie.201403102 
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article
    ​ ​Discovery of Novel Human Aquaporin-1 Blockers​
    Seeliger, D.; Zapater, C.; Krenc, D.; Haddoub, R.; Flitsch, S.; Beitz, E. & Cerdà, J. et al.​ (2013) 
    ACS Chemical Biology, 8(1) pp. 249​-256​.​ DOI: https://doi.org/10.1021/cb300153z 
    ​Details  DOI 
  • 2012 | Journal Article
    ​ ​Specificity Profiles for DNA-Binding Proteins from Exhaustive In-Silico Screening​
    Seeliger, D.; Buelens, F. P.; Goette, M.; de Groot, B. L.   & Grubmüller, H. ​ (2012) 
    Biophysical Journal, 102(3) pp. 73a​.​ DOI: https://doi.org/10.1016/j.bpj.2011.11.429 
    ​Details  DOI 
  • 2012 | Journal Article
    ​ ​Non-Equilibrium Free Energy Calculations for Ligand Optimization​
    Gapsys, V. ; Seeliger, D. & de Groot, B. L. ​ (2012) 
    Biophysical Journal, 102(3) pp. 40a​.​ DOI: https://doi.org/10.1016/j.bpj.2011.11.249 
    ​Details  DOI 
  • 2012 | Journal Article
    ​ ​New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations​
    Gapsys, V. ; Seeliger, D. & de Groot, B. L. ​ (2012) 
    Journal of Chemical Theory and Computation, 8(7) pp. 2373​-2382​.​ DOI: https://doi.org/10.1021/ct300220p 
    ​Details  DOI 
  • 2011 | Journal Article | Research Paper
    ​ ​Towards computional specificity screening of DNA-binding proteins​
    Seeliger, D.; Buelens, F. P.; Goette, M.; Groot, B. L. de   & Grubmüller, H. ​ (2011) 
    Nucleic Acids Research, 39(19) pp. 8281​-8290​.​ DOI: https://doi.org/10.1093/nar/gkr531 
    ​Details  DOI  PMID  PMC  WoS 
  • 2010 | Journal Article
    ​ ​The thermodynamic influence of trapped water molecules on a protein-ligand interaction​
    Stegmann, C. M.; Seeliger, D.; Sheldrick, G. M. ; de Groot, B. L.   & Wahl, M. C. ​ (2010) 
    Acta Crystallographica. Section A, Foundations and Advances, 66(a1) pp. s19​-s19​.​ DOI: https://doi.org/10.1107/S0108767310099599 
    ​Details  DOI 
  • 2010 | Journal Article
    ​ ​Protein Thermostability Calculations Using Alchemical Free Energy Simulations​
    Seeliger, D. & de Groot, B. L. ​ (2010) 
    Biophysical Journal, 98(10) pp. 2309​-2316​.​ DOI: https://doi.org/10.1016/j.bpj.2010.01.051 
    ​Details  DOI 
  • 2010 | Journal Article
    ​ ​Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations​
    Seeliger, D. & de Groot, B. L. ​ (2010) 
    PLoS Computational Biology, 6(1) pp. e1000634​.​ DOI: https://doi.org/10.1371/journal.pcbi.1000634 
    ​Details  DOI 
  • 2010 | Journal Article
    ​ ​Conformational Transitions Upon Ligand Binding: Holo Structure Prediction from Apo Conformations​
    Seeliger, D. & de Groot, B. L. ​ (2010) 
    Biophysical Journal, 98(3) pp. 428a​.​ DOI: https://doi.org/10.1016/j.bpj.2009.12.2318 
    ​Details  DOI 
  • 2010 | Journal Article | 
    ​ ​Ligand docking and binding site analysis with PyMOL and Autodock/Vina​
    Seeliger, D. & de Groot, B. L. ​ (2010) 
    Journal of Computer-Aided Molecular Design, 24(5) pp. 417​-422​.​ DOI: https://doi.org/10.1007/s10822-010-9352-6 
    ​Details  DOI 
  • 2009 | Journal Article
    ​ ​tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules​
    Seeliger, D. & de Groot, B. L. ​ (2009) 
    Journal of Computational Chemistry, 30(7) pp. 1160​-1166​.​ DOI: https://doi.org/10.1002/jcc.21127 
    ​Details  DOI 
  • 2009 | Journal Article
    ​ ​The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction​
    Stegmann, C. M.; Seeliger, D.; Sheldrick, G. M. ; de Groot, B. L.   & Wahl, M. C. ​ (2009) 
    Angewandte Chemie International Edition, 48(28) pp. 5207​-5210​.​ DOI: https://doi.org/10.1002/anie.200900481 
    ​Details  DOI  PMID  PMC  WoS 
  • 2008 | Journal Article
    ​ ​The Molecular Mechanism of Toxin-Induced Conformational Changes in a Potassium Channel: Relation to C-Type Inactivation​
    Zachariae, U.; Schneider, R. ; Velisetty, P.; Lange, A. ; Seeliger, D.; Wacker, S. J. & Karimi-Nejad, Y. et al.​ (2008) 
    Structure, 16(5) pp. 747​-754​.​ DOI: https://doi.org/10.1016/j.str.2008.01.018 
    ​Details  DOI 
  • 2007 | Journal Article
    ​ ​Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps​
    Seeliger, D. & de Groot, B. L. ​ (2007) 
    Proteins, 68(3) pp. 595​-601​.​ DOI: https://doi.org/10.1002/prot.21447 
    ​Details  DOI 
  • 2007 | Journal Article
    ​ ​Geometry-Based Sampling of Conformational Transitions in Proteins​
    Seeliger, D.; Haas, J. & de Groot, B. L. ​ (2007) 
    Structure, 15(11) pp. 1482​-1492​.​ DOI: https://doi.org/10.1016/j.str.2007.09.017 
    ​Details  DOI 

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