SÁNCHEZ IGNACIO E.; GALPERN, EZEQUIEL A.; FERREIRO, DIEGO U.

Solvent constraints for biopolymer folding and evolution in extraterrestrial environments

Proceedings of the National Academy of Sciences of the United States of America; Año: 2024 vol. 121

PARRA, R GONZALO; FREIBERGER, MARIA I; POLEY-GIL, MIRIAM; FERNANDEZ-MARTIN, MIGUEL; RADUSKY, LEANDRO G; RUIZ-SERRA, VICTORIA; WOLYNES, PETER G; FERREIRO, DIEGO U; VALENCIA, ALFONSO

Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families

NUCLEIC ACIDS RESEARCH; Año: 2024

FREIBERGER, MARIA I.; RUIZ-SERRA, VICTORIA; PONTES, CAMILA; ROMERO-DURANA, MIGUEL; GALAZ-DAVISON, PABLO; RAMÍREZ-SARMIENTO, CESAR A.; SCHUSTER, CLAUDIO D.; MARTI, MARCELO A.; WOLYNES, PETER G.; FERREIRO, DIEGO U.; PARRA, R. GONZALO; VALENCIA, ALFONSO

Local energetic frustration conservation in protein families and superfamilies

NATURE COMMUNICATIONS; Año: 2023 vol. 14

APTEKMANN, A.A.; BUONGIORNO, J.; GIOVANNELLI, D.; GLAMOCLIJA, M.; FERREIRO, D.U.; BROMBERG, Y.

mebipred: identifying metal-binding potential in protein sequence

BIOINFORMATICS (OXFORD, ENGLAND); Año: 2022 vol. 38 p. 3532 - 3540

SANCHES, MURILO N.; PARRA, R. GONZALO; VIEGAS, RAFAEL G.; OLIVEIRA, ANTONIO B.; WOLYNES, PETER G.; FERREIRO, DIEGO U.; LEITE, VITOR B.P.

Resolving the fine structure in the energy landscapes of repeat proteins

QRB Discovery; Año: 2022 vol. 3

SÁNCHEZ, IGNACIO E.; GALPERN, EZEQUIEL A.; GARIBALDI, MARTÍN M.; FERREIRO, DIEGO U.

Molecular Information Theory Meets Protein Folding

JOURNAL OF PHYSICAL CHEMISTRY B - (Print); Año: 2022 vol. 126 p. 8655 - 8668

GALAZ-DAVISON, PABLO; FERREIRO, DIEGO U.; RAMÍREZ-SARMIENTO, CÉSAR A.

Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors

PROTEIN SCIENCE; Año: 2022 vol. 31

GALPERN, EZEQUIEL A.; MARCHI, JACOPO; MORA, THIERRY; WALCZAK, ALEKSANDRA M.; FERREIRO, DIEGO U.

Evolution and folding of repeat proteins

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA; Año: 2022 vol. 119

BROMBERG, YANA; APTEKMANN, ARIEL A.; MAHLICH, YANNICK; COOK, LINDA; SENN, STEFAN; MILLER, MAXIMILLIAN; NANDA, VIKAS; FERREIRO, DIEGO U.; FALKOWSKI, PAUL G.

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Science Advances; Año: 2022 vol. 8

GIANNI, STEFANO; FREIBERGER, MARÍA INÉS; JEMTH, PER; FERREIRO, DIEGO U.; WOLYNES, PETER G.; FUXREITER, MONIKA

Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly

ACCOUNTS OF CHEMICAL RESEARCH; Año: 2021 vol. 54 p. 1251 - 1259

FREIBERGER, MARIA I.; WOLYNES, PETER G.; FERREIRO, DIEGO U.; FUXREITER, MONIKA

Frustration in fuzzy protein complexes leads to interaction versatility

JOURNAL OF PHYSICAL CHEMISTRY B - (Print); Año: 2021 vol. 125 p. 2513 - 2520

ATILIO O RAUSCH; MARIA I FREIBERGER; CESAR O LEONETTI; DIEGO M LUNA; LEANDRO G RADUSKY; PETER G WOLYNES; DIEGO U FERREIRO; R GONZALO PARRA

FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations

BIOINFORMATICS (OXFORD, ENGLAND); Lugar: Oxford; Año: 2021 vol. 37 p. 3038 - 3040

GALPERN, EZEQUIEL A.; FREIBERGER, MARÍA I.; FERREIRO, DIEGO U.

Large Ankyrin repeat proteins are formed with similar and energetically favorable units

PLOS ONE; Año: 2020 vol. 15

CHEN, MINGCHEN; CHEN, XUN; SCHAFER, NICHOLAS P.; CLEMENTI, CECILIA; KOMIVES, ELIZABETH A.; FERREIRO, DIEGO U.; WOLYNES, PETER G.

Surveying biomolecular frustration at atomic resolution

NATURE COMMUNICATIONS; Año: 2020 vol. 11

MARCHI, JACOPO; GALPERN, EZEQUIEL A.; ESPADA, ROCIO; FERREIRO, DIEGO U.; WALCZAK, ALEKSANDRA M.; MORA, THIERRY

Size and structure of the sequence space of repeat proteins

PLOS COMPUTATIONAL BIOLOGY; Año: 2019 vol. 15

FREIBERGER, MARIA I.; BRENDA GUZOVSKY, A.; WOLYNES, PETER G.; GONZALO PARRA, R.; FERREIRO, DIEGO U.

Local frustration around enzyme active sites

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA; Año: 2019 vol. 116 p. 4037 - 4043

A. BRENDA GUZOVSKY; SCHAFER NP; WOLYNES PG; FERREIRO DU

Localization of Energetic Frustration in Proteins

METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.); Año: 2018

FERREIRO DU; KOMIVES EA; WOLYNES PG

Frustration, function and folding

CURRENT OPINION IN STRUCTURAL BIOLOGY; Lugar: Londres; Año: 2018

TURJANSKI, PABLO; FERREIRO, DIEGO U.

On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences

JOURNAL OF PHYSICAL CHEMISTRY B - (Print); Año: 2018 vol. 122 p. 11295 - 11301

ESPADA, ROCIO; PARRA, R. GONZALO; MORA, THIERRY; WALCZAK, ALEKSANDRA M.; FERREIRO, DIEGO U.

Inferring repeat-protein energetics from evolutionary information

PLOS COMPUTATIONAL BIOLOGY; Año: 2017 vol. 13

ESPADA, ROCÍO; FERREIRO, DIEGO U.; PARRA, R. GONZALO

The Design of Repeat Proteins: Stability Conflicts with Functionality

Biochemistry & Molecular Biology Journal; Lugar: Delaware; Año: 2017 vol. 3 p. 1 - 5

FERREIRO DU; KOMIVES EA; WOLYNES PG

Frustration, function and folding

CURRENT OPINION IN STRUCTURAL BIOLOGY; Lugar: Londres; Año: 2017

POTOYAN DA; ZHENG W; FERREIRO DU; WOLYNES PG; KOMIVES EA

PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites.

JOURNAL OF PHYSICAL CHEMISTRY B - (Print); Lugar: Washington; Año: 2016

PARRA RG; SCHAFER NP; RADUSKY L; 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; Lugar: Oxford; Año: 2016

ESPADA, ROCÍO; SÁNCHEZ, IGNACIO E.; FERREIRO, DIEGO U.

Detailing Protein Landscapes under Pressure

BIOPHYSICAL JOURNAL; Año: 2016 vol. 111 p. 2339 - 2341

TURJANSKI, P; PARRA RG; ESPADA R; BECHER V; FERREIRO DU

Protein Repeats from First Principles

Scientific Reports; Año: 2016 vol. 6

ESPADA, R; PARRA, RG; MORA, T; WALCZAK, AM; FERREIRO, DU

Capturing coevolutionary signals in repeat proteins

BMC BIOINFORMATICS; Lugar: Londres; Año: 2015 vol. 16 p. 207 - 217

PARRA, RG; ESPADA, R; VERSTRAETE, N; FERREIRO, DU

Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

PLOS COMPUTATIONAL BIOLOGY; Lugar: San Francisco; Año: 2015

ESPADA, R; PARRA, RG; SIPPL M; MORA, T; WALCZAK, AM; FERREIRO, DU

Repeat Proteins challenge the concept of structural domains

BIOCHEMICAL SOCIETY TRANSACTIONS; Lugar: Londres; Año: 2015

FERREIRO, DU

Repitamos juntos: las proteínas son mosaicos

QUíMICA VIVA; Lugar: Buenos Aires; Año: 2015 vol. 14

FERREIRO DU; KOMIVES EA; WOLYNES PG

Frustration in Biomolecules

QUARTERLY REVIEWS OF BIOPHYSICS.; Lugar: Cambridge; Año: 2014 vol. 47 p. 285 - 363

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; Lugar: Oxford; Año: 2014 vol. 31 p. 2905 - 2912

PARRA RG; ESPADA R; SÁNCHEZ IE; SIPPL M; FERREIRO DU

Detecting repetitions and periodicities in proteins by tiling the structural space

JOURNAL OF PHYSICAL CHEMISTRY B - (Print); Lugar: Washington; Año: 2013 vol. 117 p. 12887 - 12897

JENIK M; PARRA RG; RADUSKY L; TURJANSKI A; WOLYNES PG; FERREIRO DU

Protein Frustratometer Server: a tool to localize the energetic frustration in protein molecules

NUCLEIC ACIDS RESEARCH; Lugar: Oxford; Año: 2012 p. 348 - 351

ROMAN EA; FARAJ SE; GALLO M; SALVAY AG; FERREIRO DU; SANTOS J

Protein stability and dynamics modulation: the case of human frataxin.

PLOS ONE; Lugar: San Francisco; Año: 2012 vol. 7 p. 45743 - 457749

CRAIG PO; LATZER 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; Lugar: Washington; Año: 2011 vol. 133 p. 17463 - 17472

DEVRIES I; FERREIRO DU; SÁNCHEZ IE; KOMIVES EA

Folding Kinetics of the Cooperatively Folded Subdomain of the I-kappa-B-alpha Ankyrin Repeat Domain

JOURNAL OF MOLECULAR BIOLOGY; Año: 2011 vol. 408 p. 163 - 176

SÁNCHEZ IE; FERREIRO DU; DE PRAT-GAY G

Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding

PROTEIN ENGINEERING DESIGN & SELECTION; Año: 2011 vol. 24 p. 179 - 184

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; Año: 2011 vol. 109 p. 3499 - 3503

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; Año: 2010 vol. 107 p. 7751 - 7756

FERREIRO DU, KOMIVES EA.

Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha.

BIOCHEMISTRY; Año: 2010 vol. 49 p. 1560 - 1567

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; Año: 2009 vol. 91 p. 432 - 443

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; Año: 2008 vol. 4 p. 1000070 - 1000070

BARRICK D, FERREIRO DU, KOMIVES EA.

Folding landscapes of ankyrin repeat proteins: experiments meet theory.

CURRENT OPINION IN STRUCTURAL BIOLOGY; Año: 2008 vol. 18 p. 27 - 34

FERREIRO DU, SÁNCHEZ IE, DE PRAT GAY G.

Ferreiro DU, Wolynes PG.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA; Año: 2008 vol. 105 p. 10797 - 10802

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; Año: 2008 vol. 105 p. 9853 - 9854

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; Año: 2008 vol. 4 p. 1000070 - 1000070

FERREIRO DU, CERVANTES CF, TRUHLAR SM, CHO SS, WOLYNES PG, KOMIVES EA.

Stabilizing IkappaBalpha by "consensus" design.

JOURNAL OF MOLECULAR BIOLOGY; Año: 2007 vol. 365 p. 1201 - 1216

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; Año: 2007 vol. 104 p. 19825 - 19830

FERREIRO DU, KOMIVES EA.

The plastic landscape of repeat proteins.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA; Año: 2007 vol. 104 p. 7735 - 7736

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; Año: 2007 vol. 104 p. 19819 - 19824

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; Año: 2006 vol. 45 p. 15520 - 15528

FERREIRO DU, DELLAROLE M, NADRA AD, DE PRAT-GAY G.

Free energy contributions to direct readout of a DNA sequence.

JOURNAL OF BIOLOGICAL CHEMISTRY; Año: 2005 vol. 280 p. 32480 - 32484

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; Año: 2005 vol. 351 p. 672 - 682

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; Año: 2005 vol. 354 p. 679 - 692

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; Año: 2003 vol. 42 p. 6218 - 6227

FERREIRO DU, DE PRAT-GAY G.

A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways.

JOURNAL OF MOLECULAR BIOLOGY; Año: 2003 vol. 331 p. 89 - 99

FERREIRO DU, LIMA LM, NADRA AD, ALONSO LG, GOLDBAUM FA, DE PRAT-GAY G.

Distinctive cognate sequence discrimination, bound DNA conformation, and binding modes in the E2 C-terminal domains from prototype human and bovine papillomaviruses

BIOCHEMISTRY; Año: 2000 vol. 39 p. 14692 - 14701

GEREMIA RA, ROUX M, FERREIRO DU, DAUPHIN-DUBOIS R, LELLOUCH AC, IELPI L.

Expression and biochemical characterisation of recombinant AceA, a bacterial alpha-mannosyltransferase

MOLECULAR AND GENERAL GENETICS; Año: 1999 vol. 261 p. 933 - 940

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; Año: 1998 vol. 180 p. 1607 - 1617