Journal of Computer-Aided Molecular Design

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  • 2023 | Journal Article | 
    ​ ​Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations​
    Stampolaki, M.; Stylianakis, I.; Zgurskaya, H. I. & Kolocouris, A.​ (2023) 
    Journal of Computer-Aided Molecular Design, 37(5-6) pp. 245​-264​.​ DOI: https://doi.org/10.1007/s10822-023-00504-6 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations​
    Rizzi, A.; Jensen, T.; Slochower, D. R.; Aldeghi, M.; Gapsys, V. ; Ntekoumes, D. & Bosisio, S. et al.​ (2020) 
    Journal of Computer-Aided Molecular Design, 34(5) pp. 601​-633​.​ DOI: https://doi.org/10.1007/s10822-020-00290-5 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software​
    Khalak, Y.; Tresadern, G.; de Groot, B. L.   & Gapsys, V. ​ (2020) 
    Journal of Computer-Aided Molecular Design, 35(1) pp. 49​-61​.​ DOI: https://doi.org/10.1007/s10822-020-00359-1 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset​
    Elisée, E.; Gapsys, V. ; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L.   & Iorga, B. I.​ (2019) 
    Journal of Computer-Aided Molecular Design, 33(12) pp. 1031​-1043​.​ DOI: https://doi.org/10.1007/s10822-019-00232-w 
    ​Details  DOI 
  • 2014 | Journal Article
    ​ ​Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies​
    Mikulskis, P.; Cioloboc, D.; Andrejic, M.; Khare, S.; Brorsson, J.; Genheden, S. & Mata, R. A.  et al.​ (2014) 
    Journal of Computer-Aided Molecular Design, 28(4) pp. 375​-400​.​ DOI: https://doi.org/10.1007/s10822-014-9739-x 
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article | 
    ​ ​Computational analysis of local membrane properties​
    Gapsys, V. ; de Groot, B. L.   & Briones, R. ​ (2013) 
    Journal of Computer-Aided Molecular Design, 27(10) pp. 845​-858​.​ DOI: https://doi.org/10.1007/s10822-013-9684-0 
    ​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 

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