1. Patel JS, Ytreberg FM, Fast Calculation of Protein-Protein Binding Free Energies using Umbrella Sampling with a Coarse-Grained Model, J Chem Theory Comput, 14:991-997 (2018) doi:10.1021/acs.jctc.7b00660
  2. Patel JS, Brown CJ, Ytreberg FM, Stenkamp DL, Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations, PLoS Comput Biol 14:e1005974 (2018) doi:10.1371/journal.pcbi.1005974
  3. Douglas SM, Chubiz LM, Harcombe WR, Ytreberg FM, Marx CJ, Parallel mutations result in a wide range of cooperation and community consequences in a two-species bacterial consortium, PLoS One, 11:e0161837 (2016) doi:10.1371/journal.pone.0161837
  4. Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM, New perspectives on Ebola virus evolution, PLoS One, 11:e0160410 (2016) doi:10.1371/journal.pone.0160410
  5. Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Wichman HA, Brown CJ, Ytreberg FM, Initiating a watch list for Ebola virus antibody escape mutations, PeerJ, 4:e1674-1-17 (2016) doi:10.7717/peerj.1674
  6. Ytreberg FM, Borcherds W, Wu H, Daughdrill GW, Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure, Intrinsically Disord Proteins, 3:1-10 (2015) doi:10.4161/21690707.2014.984565
  7. Zhan Y, Ytreberg FM, The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans, Arch Biochem Biophys, 575:22-29 (2015) doi:10.1016/
  8. Miller CR, Lee KH, Wichman HA, Ytreberg FM, Changing folding and binding stability in a viral coat protein: A comparison between substitutions accessible through mutation and those fixed by natural selection, PLoS One, 9:e112988 (2014) doi:10.1371/journal.pone.0112988
  9. Corti G, Zhan Y, Wang L, Hare B, Cantrell T, Beaux II M, Prakash T, Ytreberg FM, Miller MA, McIlroy DN, Nanoscale Geometry and Spillover on Room Temperature Storage of Hydrogen on Silica Nanosprings, J Phys D Appl Phys, 46:505307 (2013) doi:10.1088/0022-3727/46/50/505307
  10. Zhan YA, Wu H, Powell AT, Daughdrill GW, Ytreberg FM, Impact of the K24N mutation on the transactivation domain of p53 and its binding to MDM2, Proteins, 81:1738-1747 (2013) doi:10.1002/prot.24310
  11. Schramm RD, Li S, Harris BS, Rounds RP, Burgess RW, Ytreberg FM, Fuerst PG, A novel mouse Dscam mutation inhibits localization and shedding of DSCAM, PLoS One, 7:e52652 (2012) doi:10.1371/journal.pone.0052652
  12. Pina JE, Lee KH, Ytreberg FM, Effects of the Binding of Calcium Ions on the Structure and Dynamics of the PhiX174 Virus Investigated Using Molecular Dynamics, J Biol Phys, 38:397-404 (2012) doi:10.1007/s10867-011-9260-6
  13. Lee KH, Ytreberg FM, Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure, Entropy, 14:630-641 (2012) doi:10.3390/e14040630
  14. Daughdrill GW, Kashtanov S, Stancik A, Hill S, Helms G, Muschol M, Receveur-Brechot V, Ytreberg FM, Understanding the Structural Ensembles of a Highly Extended Disordered Protein, Mol BioSyst, 8:308-319 (2012) doi:10.1039/C1MB05243H
  15. Lee KH, Miller CR, Nagel AC, Wichman HA, Joyce P, Ytreberg FM, First-step mutations for adaptation at elevated temperature increase capsid stability in a virus, PLoS One, 6:e25640-1-8 (2011) doi:10.1371/journal.pone.0025640
  16. Ostergaard ME, Kumar P, Baral B, Guenther DC, Ytreberg FM, Deobald L, Paszczynski AJ, Sharma PK, and Hrdlicka PJ, C5-Functionalized DNA, LNA and alpha;-L-LNA: Positional control of polarity-sensitive fluorophores facilitates improved SNP-typing, Chem Eur J 17:3157-3165 (2011) doi:10.1002/chem.201002109
  17. Faulkner BE, Ytreberg FM, Understanding Bernoulli's principle through kinetic theory simulation, Am J Phys 79:214-216 (2011) doi:10.1119/1.3533216
  18. Shyu C, Cavileer TD, Nagler JJ, Ytreberg FM, Computational Estimation of Rainbow Trout Estrogen Receptor Binding Affinities, Toxicol Appl Pharm 250:322-326 (2011) doi:10.1016/j.taap.2010.11.005
  19. Shyu C, Ytreberg FM, Accurate Estimation of Solvation Free Energy Using Polynomial Fitting Techniques, J Comput Chem 32:134-141 (2011) doi:10.1002/jcc.21609
  20. Ytreberg FM, Computational study of small molecule binding for both tethered and free conditions, J Phys Chem B 114:5431-5434 (2010) doi:10.1021/jp911704n
  21. Shyu C, Brown CJ, Ytreberg FM, Computational study of evolutionary selection pressure on rainbow trout estrogen receptors, PLoS One e9392-1-7 (2010) doi:10.1371/journal.pone.0009392
  22. Shyu C, Ytreberg FM, Reducing the bias and uncertainty of free energy estimates by using polynomial regression to analyze thermodynamic integration data, J Comput Chem 30:2297-2304 (2009) doi:10.1002/jcc.21231
  23. Ytreberg FM, Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations, J Chem Phys 130:164906-1-8 (2009) doi:10.1063/1.3119261
  24. Ytreberg FM, Zuckerman DM, A "black-box" re-weighting analysis can correct flawed simulation data, Proc Natl Acad Sci USA 105:7982-7987 (2008) doi:10.1073/pnas.0706063105
  25. Ytreberg FM, Aroutioutian SK, Zuckerman DM, Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model, J Chem Theory Comput 3:1860-1866 (2007) doi:10.1021/ct700076t
  26. Ytreberg FM, Zuckerman DM, Swendsen RH, Comparison of free energy methods for molecular systems, J Chem Phys 125:184114-1-11 (2006) doi:10.1063/1.2378907
  27. Ytreberg FM, Zuckerman DM, Simple estimation of absolute free energies for biomolecules, J Chem Phys 124:104105-1-9 (2006) doi:10.1063/1.2174008
  28. Lyman E, Ytreberg FM, Zuckerman DM, Resolution exchange simulation, Phys Rev Lett 96:028105-1-4 (2006) doi:10.1103/PhysRevLett.96.028105
  29. Ytreberg FM, Zuckerman DM, Peptide conformational equilibria computed via a single-stage shifting protocol, J Phys Chem B 109:9096-9103 (2005) doi:10.1021/jp0510692
  30. Ytreberg FM, Zuckerman DM, Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems, J Comput Chem 25:1749-1759 (2004) doi:10.1002/jcc.20103
  31. Ytreberg FM, Zuckerman DM, Single-ensemble nonequilibrium path-sampling estimates of free energy differences, J Chem Phys 120:10876-10879 (2004) doi:10.1063/1.1760511
  32. Ytreberg FM, McKay SR, Calculated properties of field-induced aggregates in ferrofluids, Phys Rev E 61:4107-4110 (2000) doi:10.1103/PhysRevE.61.4107
  33. Ytreberg FM, McKay SR, A second mechanism for transitions in a reaction diffusion system, Phys Rev E 59:3376-3381 (1999) doi:10.1103/PhysRevE.59.3376


  1. Kashtanov S, Borcherds W, Wu H, Daughdrill GW, Ytreberg FM, Intrinsically Disordered Proteins: Volume I. Experimental Techniques (Humana Press Inc: New York, 2012)


  1. Ytreberg FM, Using non-equilibrium simulations to estimate equilibrium binding affinities, AIP Conf Proc 978:65-74 (2008) doi:10.1063/1.2891414
  2. Ytreberg FM, McKay SR, A quasi-equilibrium analysis to predict he dependence of ferrofluid aggregate properties on field ramping rate, IEEE Trans Magn 39:2648-2650 (2003) doi:10.1109/TMAG.2003.815542