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F Marty Ytreberg - Publications

Affiliations: 
Physics University of Idaho, Moscow, ID, United States 
Area:
Molecular Physics, General Biophysics
Website:
https://www.uidaho.edu/sci/physics/people/faculty/ytreberg
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49/74 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
2022 Patel D, Haag SL, Patel JS, Ytreberg FM, Bernards MT. Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. Journal of Chemical Information and Modeling. 62: 1282-1293. PMID 35194993 DOI: 10.1021/acs.jcim.1c01104  0.654
2021 Patel D, Patel JS, Ytreberg FM. Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy. Journal of Chemical Theory and Computation. PMID 33709712 DOI: 10.1021/acs.jctc.0c01045  0.719
2020 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. PMID 32470971 DOI: 10.1371/Journal.Pone.0233509  0.37
2020 Mirabzadeh CA, Ytreberg FM. Implementation of adaptive integration method for free energy calculations in molecular systems Peerj Computer Science. 6: e264. DOI: 10.7717/Peerj-Cs.264  0.363
2020 Patel DJ, Suresh Patel J, Ytreberg FM. Testing and Improving Alchemical Methods for Protein-Protein Binding Affinity Calculation Biophysical Journal. 118: 142a. DOI: 10.1016/J.Bpj.2019.11.898  0.71
2020 Barnes J, Martin K, Miller C, Ytreberg FM. Searching for a Mechanistic Description of Pairwise Epistasis in Protein Systems Biophysical Journal. 118: 50a. DOI: 10.1016/J.Bpj.2019.11.452  0.309
2019 Martin KP, MacKenzie SM, Barnes JW, Ytreberg FM. Protein Stability in Titan's Subsurface Water Ocean. Astrobiology. PMID 31730377 DOI: 10.1089/Ast.2018.1972  0.373
2019 Martin KP, Ytreberg FM. Comparing Binding Affinity Results from Pyrosetta and Coarse-Grained Simulations Biophysical Journal. 116: 145a. DOI: 10.1016/J.Bpj.2018.11.804  0.37
2019 Barnes J, Ytreberg FM. Assessing Foldx for Predicting Protein-Protein Binding Affinity Changes Due to Multiple Mutations Biophysical Journal. 116: 336a. DOI: 10.1016/J.Bpj.2018.11.1830  0.437
2019 Suresh Patel J, Ytreberg FM. Calculation of Protein-Protein Binding Free Energies using Umbrella Sampling with Dual Resolution Water Models Biophysical Journal. 116: 291a. DOI: 10.1016/J.Bpj.2018.11.1571  0.427
2017 Patel JS, Ytreberg FM. Fast Calculation of Protein-Protein Binding Free Energies using Umbrella Sampling with a Coarse-Grained Model. Journal of Chemical Theory and Computation. PMID 29286646 DOI: 10.1016/J.Bpj.2016.11.1087  0.492
2016 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. PMID 27617746 DOI: 10.1371/Journal.Pone.0161837  0.305
2016 Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Brown CJ, Wichman HA, Ytreberg FM. Biophysical Implications of Ebola Virus Evolution Biophysical Journal. 110: 494a. DOI: 10.1016/J.Bpj.2015.11.2643  0.312
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  0.378
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  0.723
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  0.59
2014 LaPorte DR, Ytreberg FM. Understanding the Evolution of Dynamics for an Intrinsically Disordered Protein Biophysical Journal. 106: 482a. DOI: 10.1016/J.Bpj.2013.11.2720  0.377
2014 Zhan Y, Ytreberg FM. The Effect of Proline CIS Trans Isomerization on P53 MDM2 Binding Biophysical Journal. 106: 481a. DOI: 10.1016/J.Bpj.2013.11.2717  0.742
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  0.725
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  0.665
2013 Zhan Y, Ytreberg FM. Absolute Binding Affinity Calculation for MDM2 Bound to a Disordered Fragment of P53 Biophysical Journal. 104: 234a. DOI: 10.1016/J.Bpj.2012.11.1320  0.741
2013 Ytreberg FM, Kashtanov S, Borcherds W, Wu H, Daughdrill GW. De Novo Generation of Bound Structures for an Intrinsically Disordered Protein using Only Alpha Carbon Chemical Shifts Biophysical Journal. 104: 191a. DOI: 10.1016/J.Bpj.2012.11.1075  0.374
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  0.532
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  0.317
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  0.43
2012 Lee KH, Ytreberg FM. Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure Entropy. 14: 630-641. DOI: 10.3390/E14040630  0.459
2012 Kashtanov S, Ytreberg FM. Characterizing Structural Ensembles of Intrinsically Disordered Proteins Determined via a Broad Ensemble Generator with Reweighting Biophysical Journal. 102: 631a. DOI: 10.1016/J.Bpj.2011.11.3436  0.369
2012 Hao Lee K, Ytreberg FM. Sampling of Random Amino Acid Mutations: Folding and Binding Stability of Coat Proteins in a Simple Virus Biophysical Journal. 102: 456a. DOI: 10.1016/J.Bpj.2011.11.2502  0.464
2012 Ada Zhan Y, Ytreberg FM. Impact of K24N Mutation on p53TAD and its Interaction with MDM2 Biophysical Journal. 102: 447a. DOI: 10.1016/J.Bpj.2011.11.2454  0.435
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  0.528
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  0.33
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  0.321
2011 Kashtanov S, Ytreberg FM. Broad Ensemble Generator (BEG): Software to Generate Ensembles for Intrinsically Disordered Proteins Biophysical Journal. 100: 59a. DOI: 10.1016/J.Bpj.2010.12.519  0.362
2011 Lee KH, Ytreberg FM. Molecular Dynamics Study of Structural Ensembles for Peptides Bound to Gold Nanoparticles Biophysical Journal. 100: 148a. DOI: 10.1016/J.Bpj.2010.12.1013  0.456
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  0.376
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  0.314
2010 Lee KH, Ytreberg FM. Toward Understanding the Effect of Single Amino Acid Mutations on Viral Capsid Stability Biophysical Journal. 98: 655a. DOI: 10.1016/J.Bpj.2009.12.3593  0.555
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  0.426
2009 Shyu C, Ytreberg FM. Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data. Journal of Computational Chemistry. 30: 2297-304. PMID 19266482 DOI: 10.1002/Jcc.21231  0.302
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  0.373
2007 Ytreberg FM. Using non-equilibrium simulations to estimate equilibrium binding affinities Aip Conference Proceedings. 978: 65-74. DOI: 10.1063/1.2891414  0.301
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  0.307
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  0.355
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  0.351
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  0.305
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  0.302
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  0.565
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  0.592
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  0.588
Low-probability matches (unlikely to be authored by this person)
2009 Shyu C, Ytreberg FM. Numerical Techniques to Optimize Free Energy Estimation Using Thermodynamic Integration Biophysical Journal. 96: 406a. DOI: 10.1016/J.Bpj.2008.12.2068  0.299
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  0.295
2011 Shyu C, Ytreberg FM. Polynomial Fitting Techniques for Accurate Estimation of Solvation Free Energy Using Thermodynamic Integration Biophysical Journal. 100: 155a. DOI: 10.1016/J.Bpj.2010.12.1061  0.295
2018 Martin K, MacKenzie S, Barnes J, Ytreberg FM. Comparing Structure Stability between Earth and Subsurface Ocean on Titan using Molecular Dynamics Simulation Biophysical Journal. 114: 528a. DOI: 10.1016/J.Bpj.2017.11.2885  0.294
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  0.29
2018 Patel JS, Brown CJ, Ytreberg FM, Stenkamp DL. Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations. Plos Computational Biology. 14: e1005974. PMID 29364888 DOI: 10.1371/Journal.Pcbi.1005974  0.289
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  0.286
2006 Lyman E, Ytreberg FM, Zuckerman DM. Resolution exchange simulation. Physical Review Letters. 96: 028105. PMID 16486650 DOI: 10.1103/Physrevlett.96.028105  0.284
2019 Patel JS, Quates CJ, Johnson EL, Ytreberg FM. Expanding the watch list for potential Ebola virus antibody escape mutations. Plos One. 14: e0211093. PMID 30897171 DOI: 10.1371/Journal.Pone.0211093  0.279
2020 Gonzalez TR, Martin KP, Barnes JE, Patel JS, Ytreberg FM. Assessment of software methods for estimating protein-protein relative binding affinities. Plos One. 15: e0240573. PMID 33347442 DOI: 10.1371/journal.pone.0240573  0.278
2018 Suresh Patel J, Brown CJ, Ytreberg FM, Stenkamp DL. Predicting Spectral Shift in the Teleost Rh2 Cone Opsins using Molecular Dynamics Simulations Biophysical Journal. 114: 338a. DOI: 10.1016/J.Bpj.2017.11.1888  0.276
2023 Sapozhnikov Y, Patel JS, Ytreberg FM, Miller CR. Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability. Bmc Bioinformatics. 24: 426. PMID 37953256 DOI: 10.1186/s12859-023-05537-0  0.267
2004 Ytreberg FM, Zuckerman DM. Erratum: “Single-ensemble nonequilibrium path-sampling estimates of free energy differences” [J. Chem. Phys. 120, 10876 (2004)] The Journal of Chemical Physics. 121: 5022-5023. DOI: 10.1063/1.1783252  0.261
2022 Barnes JE, Miller CR, Ytreberg FM. Searching for a mechanistic description of pairwise epistasis in protein systems. Proteins. PMID 35218569 DOI: 10.1002/prot.26328  0.246
2020 Mirabzadeh CA, Ytreberg FM. Implementation of adaptive integration method for free energy calculations in molecular systems. Peerj. Computer Science. 6. PMID 33457645 DOI: 10.7717/peerj-cs.264  0.243
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  0.235
2011 Faulkner BE, Ytreberg FM. Understanding Bernoulli's principle through simulations American Journal of Physics. 79: 214-216. DOI: 10.1119/1.3533216  0.226
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  0.226
2022 Beach SS, Hull MA, Ytreberg FM, Patel JS, Miura TA. Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein. Journal of Virology. e0035322. PMID 35678603 DOI: 10.1128/jvi.00353-22  0.211
2022 Barnes JE, Lund-Andersen PK, 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. Scientific Reports. 12: 18819. PMID 36335244 DOI: 10.1038/s41598-022-23482-5  0.198
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 Biophysical Journal. 108: 227a-228a. DOI: 10.1016/J.BPJ.2014.11.1256  0.185
1996 Schildt H, Ytreberg FM, McKay SR, Christian W. C++: The Complete Reference, Second Edition Computers in Physics. 10: 549. DOI: 10.1063/1.4822498  0.18
2022 Li S, Patel JS, Yang J, Crabtree AM, Rubenstein BM, Lund-Andersen PK, Ytreberg FM, Rowley PA. Defining the HIV Capsid Binding Site of Nucleoporin 153. Msphere. e0031022. PMID 36040047 DOI: 10.1128/msphere.00310-22  0.16
2023 Taggart NT, Crabtree AM, Creagh JW, Bizarria R, Li S, de la 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 Pathogens. 19: e1011418. PMID 37285383 DOI: 10.1371/journal.ppat.1011418  0.1
2021 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 leads to bacterial growth arrest in response to elevated formaldehyde. Plos Biology. 19: e3001208. PMID 34038406 DOI: 10.1371/journal.pbio.3001208  0.08
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