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Items: 31

1.

Expanding the watch list for potential Ebola virus antibody escape mutations.

Patel JS, Quates CJ, Johnson EL, Ytreberg FM.

PLoS One. 2019 Mar 21;14(3):e0211093. doi: 10.1371/journal.pone.0211093. eCollection 2019.

2.

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations.

Patel JS, Brown CJ, Ytreberg FM, Stenkamp DL.

PLoS Comput Biol. 2018 Jan 24;14(1):e1005974. doi: 10.1371/journal.pcbi.1005974. eCollection 2018 Jan.

3.

Fast Calculation of Protein-Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model.

Patel JS, Ytreberg FM.

J Chem Theory Comput. 2018 Feb 13;14(2):991-997. doi: 10.1021/acs.jctc.7b00660. Epub 2018 Jan 16.

4.

Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium.

Douglas SM, Chubiz LM, Harcombe WR, Ytreberg FM, Marx CJ.

PLoS One. 2016 Sep 12;11(9):e0161837. doi: 10.1371/journal.pone.0161837. eCollection 2016.

5.

New Perspectives on Ebola Virus Evolution.

Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM.

PLoS One. 2016 Aug 1;11(8):e0160410. doi: 10.1371/journal.pone.0160410. eCollection 2016.

6.

Initiating a watch list for Ebola virus antibody escape mutations.

Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Wichman HA, Brown CJ, Ytreberg FM.

PeerJ. 2016 Feb 16;4:e1674. doi: 10.7717/peerj.1674. eCollection 2016.

7.

The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans.

Zhan YA, Ytreberg FM.

Arch Biochem Biophys. 2015 Jun 1;575:22-9. doi: 10.1016/j.abb.2015.03.021. Epub 2015 Apr 1.

8.

Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure.

Ytreberg FM, Borcherds W, Wu H, Daughdrill GW.

Intrinsically Disord Proteins. 2015 Feb 3;3(1):e984565. doi: 10.4161/21690707.2014.984565. eCollection 2015.

9.

Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection.

Miller CR, Lee KH, Wichman HA, Ytreberg FM.

PLoS One. 2014 Nov 18;9(11):e112988. doi: 10.1371/journal.pone.0112988. eCollection 2014.

10.

Effects of the binding of calcium ions on the structure and dynamics of the ΦX174 virus investigated using molecular dynamics.

Pina JE, Lee KH, Ytreberg FM.

J Biol Phys. 2012 Jun;38(3):397-404. doi: 10.1007/s10867-011-9260-6. Epub 2012 Jan 21.

11.

Impact of the K24N mutation on the transactivation domain of p53 and its binding to murine double-minute clone 2.

Zhan YA, Wu H, Powell AT, Daughdrill GW, Ytreberg FM.

Proteins. 2013 Oct;81(10):1738-47. doi: 10.1002/prot.24310. Epub 2013 Jul 22.

12.

A novel mouse Dscam mutation inhibits localization and shedding of DSCAM.

Schramm RD, Li S, Harris BS, Rounds RP, Burgess RW, Ytreberg FM, Fuerst PG.

PLoS One. 2012;7(12):e52652. doi: 10.1371/journal.pone.0052652. Epub 2012 Dec 26.

13.

Using chemical shifts to assess transient secondary structure and generate ensemble structures of intrinsically disordered proteins.

Kashtanov S, Borcherds W, Wu H, Daughdrill GW, Ytreberg FM.

Methods Mol Biol. 2012;895:139-52. doi: 10.1007/978-1-61779-927-3_11.

PMID:
22760318
14.

First-step mutations for adaptation at elevated temperature increase capsid stability in a virus.

Lee KH, Miller CR, Nagel AC, Wichman HA, Joyce P, Ytreberg FM.

PLoS One. 2011;6(9):e25640. doi: 10.1371/journal.pone.0025640. Epub 2011 Sep 29.

15.

Understanding the structural ensembles of a highly extended disordered protein.

Daughdrill GW, Kashtanov S, Stancik A, Hill SE, Helms G, Muschol M, Receveur-Bréchot V, Ytreberg FM.

Mol Biosyst. 2012 Jan;8(1):308-19. doi: 10.1039/c1mb05243h. Epub 2011 Oct 6.

16.

C5-functionalized DNA, LNA, and α-L-LNA: positional control of polarity-sensitive fluorophores leads to improved SNP-typing.

Østergaard ME, Kumar P, Baral B, Guenther DC, Anderson BA, Ytreberg FM, Deobald L, Paszczynski AJ, Sharma PK, Hrdlicka PJ.

Chemistry. 2011 Mar 7;17(11):3157-65. doi: 10.1002/chem.201002109. Epub 2011 Feb 15.

PMID:
21328492
17.

Computational estimation of rainbow trout estrogen receptor binding affinities for environmental estrogens.

Shyu C, Cavileer TD, Nagler JJ, Ytreberg FM.

Toxicol Appl Pharmacol. 2011 Feb 1;250(3):322-6. doi: 10.1016/j.taap.2010.11.005. Epub 2010 Nov 12.

18.

Accurate estimation of solvation free energy using polynomial fitting techniques.

Shyu C, Ytreberg FM.

J Comput Chem. 2011 Jan 15;32(1):134-41. doi: 10.1002/jcc.21609.

19.

Computational study of small molecule binding for both tethered and free conditions.

Ytreberg FM.

J Phys Chem B. 2010 Apr 29;114(16):5431-4. doi: 10.1021/jp911704n.

20.

Computational study of evolutionary selection pressure on rainbow trout estrogen receptors.

Shyu C, Brown CJ, Ytreberg FM.

PLoS One. 2010 Mar 9;5(3):e9392. doi: 10.1371/journal.pone.0009392.

21.

Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations.

Ytreberg FM.

J Chem Phys. 2009 Apr 28;130(16):164906. doi: 10.1063/1.3119261.

22.

Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data.

Shyu C, Ytreberg FM.

J Comput Chem. 2009 Nov 15;30(14):2297-304. doi: 10.1002/jcc.21231.

PMID:
19266482
23.

A black-box re-weighting analysis can correct flawed simulation data.

Ytreberg FM, Zuckerman DM.

Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):7982-7. doi: 10.1073/pnas.0706063105.

24.

Demonstrated Convergence of the Equilibrium Ensemble for a Fast United-Residue Protein Model.

Ytreberg FM, Aroutiounian SKh, Zuckerman DM.

J Chem Theory Comput. 2007 Sep;3(5):1860-6. doi: 10.1021/ct700076t.

PMID:
26627628
25.

Comparison of free energy methods for molecular systems.

Ytreberg FM, Swendsen RH, Zuckerman DM.

J Chem Phys. 2006 Nov 14;125(18):184114. Review.

PMID:
17115745
26.

Peptide conformational equilibria computed via a single-stage shifting protocol.

Ytreberg FM, Zuckerman DM.

J Phys Chem B. 2005 May 12;109(18):9096-103.

PMID:
16852082
27.

Simple estimation of absolute free energies for biomolecules.

Ytreberg FM, Zuckerman DM.

J Chem Phys. 2006 Mar 14;124(10):104105.

PMID:
16542066
28.

Resolution exchange simulation.

Lyman E, Ytreberg FM, Zuckerman DM.

Phys Rev Lett. 2006 Jan 20;96(2):028105. Epub 2006 Jan 18.

PMID:
16486650
29.

Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems.

Ytreberg FM, Zuckerman DM.

J Comput Chem. 2004 Nov 15;25(14):1749-59.

PMID:
15362132
30.

Single-ensemble nonequilibrium path-sampling estimates of free energy differences.

Ytreberg FM, Zuckerman DM.

J Chem Phys. 2004 Jun 15;120(23):10876-9. Erratum in: J Chem Phys. 2004 Sep 8;121(10):5022-3.

PMID:
15268117
31.

Calculated properties of field-induced aggregates in ferrofluids

Ytreberg FM, McKay SR.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Apr;61(4 Pt B):4107-10.

PMID:
11088204

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