Samuel Genheden

Researcher

Research interests

Theoretical calculations and modelling of biomolecules.
Drug design.
Simulation techniques.


Current research projects

  • MM/GBSA and alchemical calculations on different systems
  • Evaluation of various terms in the MM/GBSA method
  • Calculation of entropies
  • Quantum mechanical approaches to ligand binding
  • Homology modeling

Publications

Researcher ID

  1. Diehl, C., Genheden, S., Modig, K., Ryde, U., Akke, M. (2009) Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3. J. Biomol. NMR, DOI: 10.1007/s10858-009-9356-5
  2. Genheden, S., Ryde, U. (2010) How to obtain statistically converged MM/GBSA results. J. Comput Chem., DOI: 10.1002/jcc.21366
  3. Söderhjelm, P., Kongsted, J., Genheden, S., Ryde, U. (2010) Estimates of ligand-binding affinities supported by quantum mechanical methods. Interdisciplinary Sciences: Computational Life Sciences , 4. DOI: 10.1007/s12539-010-0083-0
  4. Genheden, S., Ryde, U. (2011) A Comparison of Different Initialization Protocols to Obtain Statistically Independent Molecular Dynamics Simulations. J. Comput. Chem. , DOI: 10.1002/jcc.21546
  5. Genheden, S., Luchko, T., Gusarov, S., Kovalenko, A., Ryde, U. (2010) An MM/3D-RISM approach for ligand-binding affinities, J. Phys. Chem. B, DOI: 10.1021/jp101461s
  6. Genheden, S., Diehl, C., Akke, M., Ryde, U., (2010) Starting-condition dependence of order parameters derived from molecular dynamics simulations, J. Chem. Theory Comput., DOI: 10.1021/ct900696z
  7. Genheden, S., Kongsted, J., Soderhjelm, P., Ryde, U. (2010) Non-polar solvation free energies of protein-ligand complexes, J. Chem. Theory Comput., DOI: 10.1021/ct100272s
  8. Diehl, C., Engström, O., Delain, T., Håkansson, M., Genheden, S., Modig, K., Leffler, H., Ryde, U., Nilsson, U., Akke, M. (2010) Protein Flexibility and Conformational Entropy in Drug/Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3. J. Am. Chem. Soc., DOI: 10.1021/ja105852y
  9. Genheden, S., Söderhjelm, P., Ryde, U. (2011) Transferability of conformational dependent charges from protein simulations, Int. J. Quantum. Chem., DOI: 10.1002/qua.22967
  10. Genheden, S., Nilsson, I., Ryde, U. (2011) Binding affinities of factor Xa inhibitors estimated by TI and MM/GBSA, J. Chem. Inf. Model. , DOI: 10.1021/ci100458f
  11. Ciancetta A., Genheden S., Ryde U. (2011) A QM/MM study of the binding of RAPTA ligands to cathepsin B, J. Comput.-Aided Mol. Des., DOI: 10.1007/s10822-011-9448-7
  12. Genheden, S., Mikulskis, P., Hu, L.H., Kongsted, J., Söderhjelm, P., Ryde, U. (2011) Accurate estimation of non-polar solvation free energies requires explicit consideration of binding site hydration, J. Am. Chem. Soc., DOI: 10.1021/ja202972m
  13. Söderhjelm P., Genheden S., Ryde U. (2011) "Quantum mechanics in structure-based ligand design", Protein-ligand interactions, H. Gohlke, ed., Wiley & Sons, ISBN:3-527-32966-8; invited book chapter
  14. Genheden, S., Ryde, U. (2011) Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies, J. Chem. Theory Comput., DOI: 10.1021/ct200163c
  15. Saraboji K., Hakansson M., Genheden S., Diehl C., Qvist J., Weininger U., Nilsson U. J., Leffler H., Ryde U., Akke M., Logan D. T. (2001) "The carbohydrate-binding site in galectin-3 is pre-organized to recognize a sugar-like framework of oxygens: implications for drug design" Biochem., DOI: 10.1021/bi201459p
  16. Genheden, S. (2011) MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model, J. Comput.-Aided Mol. Des., DOI: 10.1007/s10822-011-9486-1
  17. Mikulskis P., Genheden S., Rydberg P., Sanderberg L., Olsen L., Ryde, U. (2012) Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods, J. Comput.-Aided Mol. Design., DOI: 10.1007/s10822-011-9524-z
  18. Genheden S., Ryde, U. (2012) Comparison of end-point continuum-solvation methods for the calculation of protein–ligand binding free energies. Proteins, DOI: 10.1002/prot.24029
  19. Mikulskis, P., Genheden S., Wichmann, K., Ryde, U. (2012) A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections. J. Comput. Chem , DOI: 10.1002/jcc.22949
  20. Genheden S., Ryde U. (2011) Improving efficiency of protein–ligand binding free-energy calculations by system truncation. J. Chem. Theory. Comput., DOI: 10.1021/ct200853g
  21. Genheden S., Ryde, U. (2011) Will molecular dynamics simulations of proteins ever reach equilibrium?, Phys. Chem. Chem. Phys. , DOI: 10.1039/C2CP23961B
  22. Genheden, S., Kuhn, O., Mikulskis, P., Hoffmann, D., U. Ryde (2012) The normal-mode enetropy in the MM/GBSA method: Effect of system truncation, buffer region, and dielectric constant" J. Chem. Inf. Model., submitted

Thesis

  • On the estimation of ligand binding affinities. Thesis in chemistry, with specialization in theoretical chemistry, Lund University, 2012. Download first 108 pages, or write to me to obtain a printed version. Errata

Talks

  • Sampl3 meeting, Stanford 2011. MM/GBSA and LIE estimates in the trypsin fragment challenge

Posters

  • Gordon conference on Computer-Aided Drug Design, Tilton 2009. How to obtain statistically converged MM/GBSA results Download
  • MolSim 2010, Amsterdam 2010. Are molecular dynamics simulations reproducible? Download
  • FLÄK meeting, Brösarp 2010. Estimating protein-ligand binding affinities Download
  • 8th European Conference on Computational Chemistry, Lund 2010. Non-polar solvation free energies of protein-ligand complexes Download
  • Gordon conference on Computational Chemistry, Les Diablerets 2010. Non-polar solvation free energies of protein-ligand complexes Download
  • 5th Theoretical Biophysics International Symposium, Madeira 2011. Improving efficiency of protein–ligand free energy calculations Download
  • Scheele Symposium, Uppsala 2011. Estimating protein-ligand binding affinities Download

Short curriculum vitae

  • PhD studies in Chemistry with specialization in theoretical chemistry, Lund University 2008-2012
  • Research visit, 5 weeks, University of Queensland, Brisbane, 2011
  • Master project in computational modelling, University of Porto, 2008
  • Master of Science in Theoretical chemistry and computational modelling, University of Orebro, 2006-2008
  • Bachelor of Science in Bioinformatics, University of Skovde, 2003-2006
Full cv

Teaching duties

  • Tutor of computer labs, Medicinal Chemistry (KEMM10), HT2008-HT2010
  • Tutor of labs in spectroscopy and titration, General and analytical chemistry (KEMA00), VT2010
  • Tutor of computer labs, Bio-inorganic Chemistry (KEMM32), HT2008
  • Tutor of computer labs in two bioinformatics courses, University of Skovde, 2005

Breakfast club

Link to the schedule of the breakfast club


Manuals

Link to manuals/guides that I have written