Publications

Sapozhnikov Y, Patel JS, Ytreberg FM, Miller CR, Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability, BMC Bioinform 24:426 (2023) doi: 10.1186/s12859-023-05537-0

Taggart NT, Crabtree AM, Creagh JW, Bizzaria R, Li S, Higuera I, Barnes JE, Shipley MA, Boyer JM, Stedman KM, Ytreberg FM, Rowley PA, Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae, PLoS Pathog 19:e1011418 (2023) doi: 10.1371/journal.ppat.1011418

Barnes JE, Lund-Andersen P, Patel JS, Ytreberg FM, The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6 Sci Rep, 12:18819 (2022) doi: 10.1038/s41598-022-23482-5

Li S, Patel JS, Yang JM, Crabtree AB,Rubenstein BM, Lund-Andersen P, Ytreberg FM, Rowley PA, Defining the HIV Capsid Binding Site of Nucleoporin 153, mSphere 7:e00310-22 (2022) doi: 10.1128/msphere.00310-22

Beach SS, Hull M, Ytreberg FM, Patel JS, Miura TA, Molecular modeling predicts novel antibody escape mutations in respiratory syncytial virus fusion glycoprotein, J Virol 96:e00353 (2022) doi: 10.1128/jvi.00353-22

Barnes JE, Miller CR, Ytreberg FM, Searching for a mechanistic description of pairwise epistasis in protein systems, Proteins 90:1474 (2022) doi: 10.1002/prot.26328

Patel D, Haag SL, Patel JS, Ytreberg FM, Bernards MT, Paired Simulations and Experimental Investigations into the Calcium-dependent Conformation of Albumin, J Chem Inf Model 62:1282 (2022) doi:10.1021/acs.jcim.1c01104

Bazurto JV, Nayak DD, Ticak T, Davlieva M, Lee JA, Hellenbrand CN, Lambert LB, Benski OJ, Quates CJ, Johnson JL, Patel JS, Ytreberg FM, Shamoo Y, Marx CJ, EfgA is a conserved formaldehyde sensor that halts bacterial translation in response to elevated formaldehyde, PLoS Biol 19:e3001208 (2021) doi:10.1371/journal.pbio.3001208

Patel D, Patel JS, Ytreberg FM, Implementing and assessing an alchemical method for calculating protein-protein binding free energy, J Chem Theory Comput 17:2457 (2021) doi:10.1021/acs.jctc.0c01045

Gonzalez TR, Martin KP, Barnes JE, Patel JE, Ytreberg FM, Assessment of software methods for estimating protein-protein relative binding affinities, PLoS One 15:e0240573 (2020) doi:10.1371/journal.pone.0240573

Yang J, Naik N, Patel JS, Wylie CS, Gu W, Huang J, Ytreberg FM, Naik MT, Weinreich DM, Rubenstein BM, Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness, PLoS One 15:e0233509 (2020) doi:10.1371/journal.pone.0233509

Mirabzadeh CA, Ytreberg FM, Implementation of adaptive integration method for free energy calculations in molecular systems, PeerJ Comput Sci 6:e264 (2020) doi: 10.7717/peerj-cs.264

Martin KP, MacKenzie SM, Barnes JW, Ytreberg FM, Protein Stability in Titan’s Subsurface Water Ocean, Astrobiology 20:190 (2020) doi:10.1089/ast.2018.1972

Patel JS, Quates CJ, Johnson EL, Ytreberg, FM, Expanding the watch list for potential Ebola virus antibody escape mutations, PLoS One 14:e0211093 (2019) doi:10.1371/journal.pone.0211093

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

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

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

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

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

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

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/j.abb.2015.03.021

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

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

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

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

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

Lee KH, Ytreberg FM, Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure, Entropy 14:630-641 (2012) doi:10.3390/e14040630

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

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

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

Faulkner BE, Ytreberg FM, Understanding Bernoulli's principle through kinetic theory simulation, Am J Phys 79:214-216 (2011) doi:10.1119/1.3533216

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

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

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

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

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

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

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

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

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

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

Lyman E, Ytreberg FM, Zuckerman DM, Resolution exchange simulation, Phys Rev Lett 96:028105-1-4 (2006) doi:10.1103/PhysRevLett.96.028105

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

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

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

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

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

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

Ytreberg FM, Using non-equilibrium simulations to estimate equilibrium binding affinities, AIP Conf Proc 978:65-74 (2008) doi:10.1063/1.2891414

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