F Marty Ytreberg - Publications

Physics University of Idaho, Moscow, ID, United States 
Molecular Physics, General Biophysics

31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM. New Perspectives on Ebola Virus Evolution. Plos One. 11: e0160410. PMID 27479005 DOI: 10.1371/Journal.Pone.0160410  0.72
2016 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. PMID 26925318 DOI: 10.7717/Peerj.1674  0.72
2015 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 Disordered Proteins. 3: e984565. PMID 28232883 DOI: 10.1016/J.Bpj.2014.11.1256  0.36
2015 Zhan YA, Ytreberg FM. The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans. Archives of Biochemistry and Biophysics. 575: 22-9. PMID 25840370 DOI: 10.1016/J.Abb.2015.03.021  0.72
2014 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. PMID 25405628 DOI: 10.1371/Journal.Pone.0112988  0.72
2013 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 murine double-minute clone 2. Proteins. 81: 1738-47. PMID 23609977 DOI: 10.1002/Prot.24310  0.72
2013 Corti G, Zhan Y, Wang L, Hare B, Cantrell T, Ii MB, Prakash T, Ytreberg FM, Miller MA, Mcilroy DN. The effects of nanoscale geometry and spillover on room temperature storage of hydrogen on silica nanosprings Journal of Physics D: Applied Physics. 46. DOI: 10.1088/0022-3727/46/50/505307  0.72
2012 Pina JE, Lee KH, Ytreberg FM. Effects of the binding of calcium ions on the structure and dynamics of the ΦX174 virus investigated using molecular dynamics. Journal of Biological Physics. 38: 397-404. PMID 23729905 DOI: 10.1007/S10867-011-9260-6  0.72
2012 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. PMID 23300735 DOI: 10.1371/Journal.Pone.0052652  0.72
2012 Kashtanov S, Borcherds W, Wu H, Daughdrill GW, Ytreberg FM. Using chemical shifts to assess transient secondary structure and generate ensemble structures of intrinsically disordered proteins. Methods in Molecular Biology (Clifton, N.J.). 895: 139-52. PMID 22760318 DOI: 10.1007/978-1-61779-927-3_11  0.36
2012 Daughdrill GW, Kashtanov S, Stancik A, Hill SE, Helms G, Muschol M, Receveur-Bréchot V, Ytreberg FM. Understanding the structural ensembles of a highly extended disordered protein. Molecular Biosystems. 8: 308-19. PMID 21979461 DOI: 10.1039/C1Mb05243H  0.72
2011 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. PMID 21980515 DOI: 10.1371/Journal.Pone.0025640  0.72
2011 Østergaard ME, Kumar P, Baral B, Guenther DC, Anderson BA, Ytreberg FM, Deobald L, Paszczynski AJ, Sharma PK, Hrdlicka PJ. C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 3157-65. PMID 21328492 DOI: 10.1002/Chem.201002109  0.72
2011 Shyu C, Cavileer TD, Nagler JJ, Ytreberg FM. Computational estimation of rainbow trout estrogen receptor binding affinities for environmental estrogens. Toxicology and Applied Pharmacology. 250: 322-6. PMID 21075131 DOI: 10.1016/J.Taap.2010.11.005  0.72
2011 Shyu C, Ytreberg FM. Accurate estimation of solvation free energy using polynomial fitting techniques. Journal of Computational Chemistry. 32: 134-41. PMID 20623657 DOI: 10.1002/Jcc.21609  0.72
2011 Faulkner BE, Ytreberg FM. Understanding Bernoulli's principle through simulations American Journal of Physics. 79: 214-216. DOI: 10.1119/1.3533216  0.72
2010 Ytreberg FM. Computational study of small molecule binding for both tethered and free conditions. The Journal of Physical Chemistry. B. 114: 5431-4. PMID 20369865 DOI: 10.1021/Jp911704N  0.72
2010 Shyu C, Brown CJ, Ytreberg FM. Computational study of evolutionary selection pressure on rainbow trout estrogen receptors. Plos One. 5: e9392. PMID 20231885 DOI: 10.1371/Journal.Pone.0009392  0.72
2009 Ytreberg FM. Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations. The Journal of Chemical Physics. 130: 164906. PMID 19405629 DOI: 10.1063/1.3119261  0.72
2008 Ytreberg FM, Zuckerman DM. A black-box re-weighting analysis can correct flawed simulation data. Proceedings of the National Academy of Sciences of the United States of America. 105: 7982-7. PMID 18544653 DOI: 10.1073/Pnas.0706063105  0.72
2007 Ytreberg FM, Aroutiounian SKh, Zuckerman DM. Demonstrated Convergence of the Equilibrium Ensemble for a Fast United-Residue Protein Model. Journal of Chemical Theory and Computation. 3: 1860-6. PMID 26627628 DOI: 10.1021/Ct700076T  0.72
2007 Ytreberg FM. Using non-equilibrium simulations to estimate equilibrium binding affinities Aip Conference Proceedings. 978: 65-74. DOI: 10.1063/1.2891414  0.72
2006 Ytreberg FM, Swendsen RH, Zuckerman DM. Comparison of free energy methods for molecular systems. The Journal of Chemical Physics. 125: 184114. PMID 17115745 DOI: 10.1063/1.2378907  0.72
2006 Ytreberg FM, Zuckerman DM. Simple estimation of absolute free energies for biomolecules. The Journal of Chemical Physics. 124: 104105. PMID 16542066 DOI: 10.1063/1.2174008  0.72
2006 Lyman E, Ytreberg FM, Zuckerman DM. Resolution exchange simulation. Physical Review Letters. 96: 028105. PMID 16486650 DOI: 10.1103/Physrevlett.96.028105  0.72
2005 Ytreberg FM, Zuckerman DM. Peptide conformational equilibria computed via a single-stage shifting protocol. The Journal of Physical Chemistry. B. 109: 9096-103. PMID 16852082 DOI: 10.1021/Jp0510692  0.72
2004 Ytreberg FM, Zuckerman DM. Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. Journal of Computational Chemistry. 25: 1749-59. PMID 15362132 DOI: 10.1002/Jcc.20103  0.72
2004 Ytreberg FM, Zuckerman DM. Single-ensemble nonequilibrium path-sampling estimates of free energy differences. The Journal of Chemical Physics. 120: 10876-9. PMID 15268117 DOI: 10.1063/1.1760511  0.72
2003 Ytreberg FM, McKay SR. Model for the effect of ramping rate on ferrofluid aggregates Digests of the Intermag Conference. DOI: 10.1109/INTMAG.2003.1230774  0.72
2000 Ytreberg FM, McKay SR. Calculated properties of field-induced aggregates in ferrofluids Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 61: 4107-10. PMID 11088204  0.72
1999 Ytreberg FM, McKay SR. Second mechanism for transitions in a reaction diffusion system Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 3376-3381. DOI: 10.1103/Physreve.59.3376  0.72
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