Samuel Genheden

Researcher

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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; DOI: 10.1002/9783527645947.ch7
  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 entropy in the MM/GBSA method: Effect of system truncation, buffer region, and dielectric constant J. Chem. Inf. Model., submitted
  23. Uranga, J., Mikulskis, P., Genheden, S., Ryde, U. (2012) Can the protonation state of histidine residues be determined from molecular dynamics simulations? Comp. & Theor. Chem., 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