| Year |
Citation |
Score |
| 2023 |
Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Local energetic frustration conservation in protein families and superfamilies. Nature Communications. 14: 8379. PMID 38104123 DOI: 10.1038/s41467-023-43801-2 |
0.53 |
|
| 2022 |
Sanches MN, Parra RG, Viegas RG, Oliveira AB, Wolynes PG, Ferreiro DU, Leite VBP. Resolving the fine structure in the energy landscapes of repeat proteins. Qrb Discovery. 3: e7. PMID 37529289 DOI: 10.1017/qrd.2022.4 |
0.621 |
|
| 2022 |
Sánchez IE, Galpern EA, Garibaldi MM, Ferreiro DU. Molecular Information Theory Meets Protein Folding. The Journal of Physical Chemistry. B. 126: 8655-8668. PMID 36282961 DOI: 10.1021/acs.jpcb.2c04532 |
0.672 |
|
| 2022 |
Galpern EA, Marchi J, Mora T, Walczak AM, Ferreiro DU. Evolution and folding of repeat proteins. Proceedings of the National Academy of Sciences of the United States of America. 119: e2204131119. PMID 35905321 DOI: 10.1073/pnas.2204131119 |
0.421 |
|
| 2022 |
Galaz-Davison P, Ferreiro DU, Ramírez-Sarmiento CA. Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors. Protein Science : a Publication of the Protein Society. 31: e4337. PMID 35634768 DOI: 10.1002/pro.4337 |
0.391 |
|
| 2022 |
Guzovsky AB, Schafer NP, Wolynes PG, Ferreiro DU. Localization of Energetic Frustration in Proteins. Methods in Molecular Biology (Clifton, N.J.). 2376: 387-398. PMID 34845622 DOI: 10.1007/978-1-0716-1716-8_22 |
0.579 |
|
| 2021 |
Rausch AO, Freiberger MI, Leonetti CO, Luna DM, Radusky LG, Wolynes PG, Ferreiro DU, Gonzalo Parra R. FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations. Bioinformatics (Oxford, England). PMID 33720293 DOI: 10.1093/bioinformatics/btab176 |
0.622 |
|
| 2021 |
Freiberger MI, Wolynes PG, Ferreiro DU, Fuxreiter M. Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility. The Journal of Physical Chemistry. B. 125: 2513-2520. PMID 33667107 DOI: 10.1021/acs.jpcb.0c11068 |
0.561 |
|
| 2021 |
Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of Chemical Research. PMID 33550810 DOI: 10.1021/acs.accounts.0c00813 |
0.593 |
|
| 2020 |
Chen M, Chen X, Schafer NP, Clementi C, Komives EA, Ferreiro DU, Wolynes PG. Surveying biomolecular frustration at atomic resolution. Nature Communications. 11: 5944. PMID 33230150 DOI: 10.1038/s41467-020-19560-9 |
0.533 |
|
| 2020 |
Galpern EA, Freiberger MI, Ferreiro DU. Large Ankyrin repeat proteins are formed with similar and energetically favorable units. Plos One. 15: e0233865. PMID 32579546 DOI: 10.1371/Journal.Pone.0233865 |
0.47 |
|
| 2019 |
Marchi J, Galpern EA, Espada R, Ferreiro DU, Walczak AM, Mora T. Size and structure of the sequence space of repeat proteins. Plos Computational Biology. 15: e1007282. PMID 31415557 DOI: 10.1371/Journal.Pcbi.1007282 |
0.428 |
|
| 2019 |
Freiberger MI, Guzovsky AB, Wolynes PG, Parra RG, Ferreiro DU. Local frustration around enzyme active sites. Proceedings of the National Academy of Sciences of the United States of America. PMID 30765513 DOI: 10.1073/Pnas.1819859116 |
0.633 |
|
| 2018 |
Turjanski P, Ferreiro DU. On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences. The Journal of Physical Chemistry. B. PMID 30239207 DOI: 10.1021/Acs.Jpcb.8B07206 |
0.37 |
|
| 2017 |
Ferreiro DU, Komives EA, Wolynes PG. Frustration, function and folding. Current Opinion in Structural Biology. 48: 68-73. PMID 29101782 DOI: 10.1016/J.Sbi.2017.09.006 |
0.572 |
|
| 2017 |
Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU. Inferring repeat-protein energetics from evolutionary information. Plos Computational Biology. 13: e1005584. PMID 28617812 DOI: 10.1371/Journal.Pcbi.1005584 |
0.542 |
|
| 2016 |
Espada R, Sánchez IE, Ferreiro DU. Detailing Protein Landscapes under Pressure. Biophysical Journal. 111: 2339-2341. PMID 27926834 DOI: 10.1016/J.Bpj.2016.10.038 |
0.709 |
|
| 2016 |
Parra RG, Schafer NP, Radusky LG, Tsai MY, Guzovsky AB, Wolynes PG, Ferreiro DU. Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics. Nucleic Acids Research. PMID 27131359 DOI: 10.1093/Nar/Gkw304 |
0.787 |
|
| 2016 |
Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA. PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites. The Journal of Physical Chemistry. B. PMID 27098223 DOI: 10.1021/Acs.Jpcb.6B02359 |
0.52 |
|
| 2016 |
Turjanski P, Parra RG, Espada R, Becher V, Ferreiro DU. Protein Repeats from First Principles. Scientific Reports. 6: 23959. PMID 27044676 DOI: 10.1038/Srep23959 |
0.488 |
|
| 2015 |
Parra RG, Espada R, Verstraete N, Ferreiro DU. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family. Plos Computational Biology. 11: e1004659. PMID 26691182 DOI: 10.1371/Journal.Pcbi.1004659 |
0.529 |
|
| 2015 |
Espada R, Parra RG, Sippl MJ, Mora T, Walczak AM, Ferreiro DU. Repeat proteins challenge the concept of structural domains. Biochemical Society Transactions. 43: 844-9. PMID 26517892 DOI: 10.1042/Bst20150083 |
0.521 |
|
| 2015 |
Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU. Capturing coevolutionary signals inrepeat proteins. Bmc Bioinformatics. 16: 207. PMID 26134293 DOI: 10.1186/S12859-015-0648-3 |
0.461 |
|
| 2014 |
Ferreiro DU, Komives EA, Wolynes PG. Frustration in biomolecules. Quarterly Reviews of Biophysics. 47: 285-363. PMID 25225856 DOI: 10.1017/S0033583514000092 |
0.619 |
|
| 2014 |
Krick T, Verstraete N, Alonso LG, Shub DA, Ferreiro DU, Shub M, Sánchez IE. Amino Acid metabolism conflicts with protein diversity. Molecular Biology and Evolution. 31: 2905-12. PMID 25086000 DOI: 10.1093/Molbev/Msu228 |
0.61 |
|
| 2013 |
Parra RG, Espada R, Sánchez IE, Sippl MJ, Ferreiro DU. Detecting repetitions and periodicities in proteins by tiling the structural space. The Journal of Physical Chemistry. B. 117: 12887-97. PMID 23758291 DOI: 10.1021/Jp402105J |
0.705 |
|
| 2012 |
Roman EA, Faraj SE, Gallo M, Salvay AG, Ferreiro DU, Santos J. Protein stability and dynamics modulation: the case of human frataxin. Plos One. 7: e45743. PMID 23049850 DOI: 10.1371/Journal.Pone.0045743 |
0.53 |
|
| 2012 |
Jenik M, Parra RG, Radusky LG, Turjanski A, Wolynes PG, Ferreiro DU. Protein frustratometer: a tool to localize energetic frustration in protein molecules. Nucleic Acids Research. 40: W348-51. PMID 22645321 DOI: 10.1093/Nar/Gks447 |
0.652 |
|
| 2011 |
Craig PO, Lätzer J, Weinkam P, Hoffman RM, Ferreiro DU, Komives EA, Wolynes PG. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. Journal of the American Chemical Society. 133: 17463-72. PMID 21913704 DOI: 10.1021/Ja207506Z |
0.707 |
|
| 2011 |
DeVries I, Ferreiro DU, Sánchez IE, Komives EA. Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain. Journal of Molecular Biology. 408: 163-76. PMID 21329696 DOI: 10.1016/J.Jmb.2011.02.021 |
0.652 |
|
| 2011 |
Ferreiro DU, Hegler JA, Komives EA, Wolynes PG. On the role of frustration in the energy landscapes of allosteric proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 3499-503. PMID 21273505 DOI: 10.1073/Pnas.1018980108 |
0.648 |
|
| 2011 |
Sánchez IE, Ferreiro DU, Gay Gde P. Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding. Protein Engineering, Design & Selection : Peds. 24: 179-84. PMID 20876193 DOI: 10.1093/Protein/Gzq064 |
0.658 |
|
| 2010 |
Sánchez IE, Ferreiro DU, Dellarole M, de Prat-Gay G. Experimental snapshots of a protein-DNA binding landscape. Proceedings of the National Academy of Sciences of the United States of America. 107: 7751-6. PMID 20375284 DOI: 10.1073/Pnas.0911734107 |
0.675 |
|
| 2010 |
Ferreiro DU, Komives EA. Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry. 49: 1560-7. PMID 20055496 DOI: 10.1021/Bi901948J |
0.336 |
|
| 2009 |
Wetzler DE, Gallo M, Melis R, Eliseo T, Nadra AD, Ferreiro DU, Paci M, Sánchez IE, Cicero DO, de Prat Gay G. A strained DNA binding helix is conserved for site recognition, folding nucleation, and conformational modulation. Biopolymers. 91: 432-43. PMID 19156829 DOI: 10.1002/Bip.21146 |
0.624 |
|
| 2008 |
Ferreiro DU, Sánchez IE, de Prat Gay G. Transition state for protein-DNA recognition. Proceedings of the National Academy of Sciences of the United States of America. 105: 10797-802. PMID 18664582 DOI: 10.1073/Pnas.0802383105 |
0.659 |
|
| 2008 |
Ferreiro DU, Wolynes PG. The capillarity picture and the kinetics of one-dimensional protein folding. Proceedings of the National Academy of Sciences of the United States of America. 105: 9853-4. PMID 18632565 DOI: 10.1073/Pnas.0805287105 |
0.637 |
|
| 2008 |
Ferreiro DU, Walczak AM, Komives EA, Wolynes PG. The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. Plos Computational Biology. 4: e1000070. PMID 18483553 DOI: 10.1371/Journal.Pcbi.1000070 |
0.672 |
|
| 2008 |
Barrick D, Ferreiro DU, Komives EA. Folding landscapes of ankyrin repeat proteins: experiments meet theory. Current Opinion in Structural Biology. 18: 27-34. PMID 18243686 DOI: 10.1016/J.Sbi.2007.12.004 |
0.532 |
|
| 2007 |
Sutto L, Lätzer J, Hegler JA, Ferreiro DU, Wolynes PG. Consequences of localized frustration for the folding mechanism of the IM7 protein. Proceedings of the National Academy of Sciences of the United States of America. 104: 19825-30. PMID 18077415 DOI: 10.1073/Pnas.0709922104 |
0.742 |
|
| 2007 |
Ferreiro DU, Hegler JA, Komives EA, Wolynes PG. Localizing frustration in native proteins and protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104: 19819-24. PMID 18077414 DOI: 10.1073/Pnas.0709915104 |
0.645 |
|
| 2007 |
Ferreiro DU, Komives EA. The plastic landscape of repeat proteins. Proceedings of the National Academy of Sciences of the United States of America. 104: 7735-6. PMID 17483477 DOI: 10.1073/Pnas.0702682104 |
0.52 |
|
| 2007 |
Ferreiro DU, Cervantes CF, Truhlar SM, Cho SS, Wolynes PG, Komives EA. Stabilizing IkappaBalpha by "consensus" design. Journal of Molecular Biology. 365: 1201-16. PMID 17174335 DOI: 10.1016/J.Jmb.2006.11.044 |
0.67 |
|
| 2006 |
Cerutti ML, Ferreiro DU, Sanguineti S, Goldbaum FA, de Prat-Gay G. Antibody recognition of a flexible epitope at the DNA binding site of the human papillomavirus transcriptional regulator E2. Biochemistry. 45: 15520-8. PMID 17176073 DOI: 10.1021/Bi0615184 |
0.389 |
|
| 2005 |
Ferreiro DU, Cho SS, Komives EA, Wolynes PG. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. Journal of Molecular Biology. 354: 679-92. PMID 16257414 DOI: 10.1016/J.Jmb.2005.09.078 |
0.743 |
|
| 2005 |
de Prat-Gay G, Nadra AD, Corrales-Izquierdo FJ, Alonso LG, Ferreiro DU, Mok YK. The folding mechanism of a dimeric beta-barrel domain. Journal of Molecular Biology. 351: 672-82. PMID 16023675 DOI: 10.1016/J.Jmb.2005.05.070 |
0.466 |
|
| 2005 |
Ferreiro DU, Dellarole M, Nadra AD, de Prat-Gay G. Free energy contributions to direct readout of a DNA sequence. The Journal of Biological Chemistry. 280: 32480-4. PMID 16000299 DOI: 10.1074/Jbc.M505706200 |
0.449 |
|
| 2003 |
Ferreiro DU, de Prat-Gay G. A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways. Journal of Molecular Biology. 331: 89-99. PMID 12875838 DOI: 10.1016/S0022-2836(03)00720-4 |
0.454 |
|
| 2003 |
Di Pietro SM, Centeno JM, Cerutti ML, Lodeiro MF, Ferreiro DU, Alonso LG, Schwarz FP, Goldbaum FA, de Prat-Gay G. Specific antibody-DNA interaction: a novel strategy for tight DNA recognition. Biochemistry. 42: 6218-27. PMID 12755625 DOI: 10.1021/Bi026866U |
0.322 |
|
| 1998 |
Katzen F, Ferreiro DU, Oddo CG, Ielmini MV, Becker A, Pühler A, Ielpi L. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. Journal of Bacteriology. 180: 1607-17. PMID 9537354 DOI: 10.1128/Jb.180.7.1607-1617.1998 |
0.302 |
|
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