| Year |
Citation |
Score |
| 2022 |
Kubelka GS, Kubelka J. Multi-Probe Equilibrium Analysis of Gradual (Un)Folding Processes. Methods in Molecular Biology (Clifton, N.J.). 2376: 161-171. PMID 34845609 DOI: 10.1007/978-1-0716-1716-8_9 |
0.336 |
|
| 2021 |
Kaminský J, Horáčková F, Biačková N, Hubáčková T, Socha O, Kubelka J. Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity. The Journal of Physical Chemistry. B. 125: 11350-11363. PMID 34612644 DOI: 10.1021/acs.jpcb.1c05480 |
0.342 |
|
| 2018 |
Lai JK, Kubelka GS, Kubelka J. Effect of Mutations on the Global and Site-Specific Stability and Folding of an Elementary Protein Structural Motif. The Journal of Physical Chemistry. B. PMID 29985619 DOI: 10.1021/Acs.Jpcb.8B05280 |
0.391 |
|
| 2017 |
Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA. A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. Proteins. PMID 29178386 DOI: 10.1002/Prot.25429 |
0.334 |
|
| 2016 |
Keiderling TA, Lakhani A, Wei Y, Vazquez F, Kubelka J, Bour P. Modeling Peptide Vibrations Local and Perturbative Contributions Biophysical Journal. 110: 209a. DOI: 10.1016/J.Bpj.2015.11.1165 |
0.745 |
|
| 2015 |
Lai JK, Kubelka GS, Kubelka J. Sequence, structure, and cooperativity in folding of elementary protein structural motifs. Proceedings of the National Academy of Sciences of the United States of America. 112: 9890-5. PMID 26216963 DOI: 10.1073/Pnas.1506309112 |
0.444 |
|
| 2015 |
Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 134: 473-83. PMID 25036456 DOI: 10.1016/J.Saa.2014.06.102 |
0.448 |
|
| 2015 |
Anderson BA, Kubelka GS, Kubelka J. Temperature dependence of peptide carboxylic group IR spectra in the amide I′ region at neutral and acidic pH Vibrational Spectroscopy. 77: 40-50. DOI: 10.1016/J.Vibspec.2015.02.005 |
0.411 |
|
| 2015 |
Chi H, Tobias F, Kessler J, Kubelka J, Bouř P, Keiderling TA. Role of Side-Chains in Forming Peptide Aggregates and Fibrils. IR and VCD Spectroscopic Studies. Theory and Experiment Biophysical Journal. 108: 523a. DOI: 10.1016/J.Bpj.2014.11.2867 |
0.725 |
|
| 2014 |
Kubelka GS, Kubelka J. Site-specific thermodynamic stability and unfolding of a de novo designed protein structural motif mapped by 13C isotopically edited IR spectroscopy. Journal of the American Chemical Society. 136: 6037-48. PMID 24684597 DOI: 10.1021/Ja500918K |
0.446 |
|
| 2014 |
Sargsyan G, Leonard BM, Kubelka J, Balaz M. Supramolecular ssDNA templated porphyrin and metalloporphyrin nanoassemblies with tunable helicity. Chemistry (Weinheim An Der Bergstrasse, Germany). 20: 1878-92. PMID 24458504 DOI: 10.1002/Chem.201304153 |
0.371 |
|
| 2014 |
Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. Biopolymers. 101: 536-48. PMID 24122549 DOI: 10.1002/Bip.22416 |
0.414 |
|
| 2014 |
Chi H, Welch WR, Kubelka J, Kessler J, Bour P, Keiderling TA. Interaction of Beta-Sheets to Form Aggregates and Fibrils. Theoretical and Experimental Spectroscopic Studies of Peptide Ir and Vcd Spectra Biophysical Journal. 106: 685a. DOI: 10.1016/J.Bpj.2013.11.3792 |
0.735 |
|
| 2014 |
Lai JK, Kubelka J. Statistical Mechanical Models for Analyzing the Site-Specific Folding of helix-turn-helix Motifs Biophysical Journal. 106: 671a-672a. DOI: 10.1016/J.Bpj.2013.11.3720 |
0.404 |
|
| 2014 |
Kubelka GS, Kubelka J. Refined Folding Mechanism of a Helix-turn-helix Motif Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.3716 |
0.41 |
|
| 2014 |
Kubelka J. A New Method for Analysis of Temperature Dependent IR Amide I Spectra of Peptides and Proteins Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.3394 |
0.51 |
|
| 2013 |
Chi H, Welch WR, Kubelka J, Keiderling TA. Insight into the packing pattern of β2 fibrils: a model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy. Biomacromolecules. 14: 3880-91. PMID 24053614 DOI: 10.1021/Bm401015F |
0.705 |
|
| 2013 |
Kubelka J. Multivariate analysis of spectral data with frequency shifts: application to temperature dependent infrared spectra of peptides and proteins. Analytical Chemistry. 85: 9588-95. PMID 24028416 DOI: 10.1021/Ac402083P |
0.504 |
|
| 2013 |
Welch WR, Kubelka J, Keiderling TA. Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory. The Journal of Physical Chemistry. B. 117: 10343-58. PMID 23924300 DOI: 10.1021/Jp4056126 |
0.676 |
|
| 2013 |
Welch WR, Keiderling TA, Kubelka J. Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations. The Journal of Physical Chemistry. B. 117: 10359-69. PMID 23924239 DOI: 10.1021/Jp405613R |
0.691 |
|
| 2013 |
Sedghi M, Goual L, Welch W, Kubelka J. Effect of asphaltene structure on association and aggregation using molecular dynamics. The Journal of Physical Chemistry. B. 117: 5765-76. PMID 23581711 DOI: 10.1021/Jp401584U |
0.333 |
|
| 2013 |
Topchiy E, Armstrong GS, Boswell KI, Buchner GS, Kubelka J, Lehmann TE. T1BT* structural study of an anti-plasmodial peptide through NMR and molecular dynamics. Malaria Journal. 12: 104. PMID 23506240 DOI: 10.1186/1475-2875-12-104 |
0.416 |
|
| 2013 |
Sargsyan G, Schatz AA, Kubelka J, Balaz M. Formation and helicity control of ssDNA templated porphyrin nanoassemblies. Chemical Communications (Cambridge, England). 49: 1020-2. PMID 23258275 DOI: 10.1039/C2Cc38150H |
0.304 |
|
| 2013 |
Welch WR, Kubelka J, Keiderling TA. DFT-Level Calculations of IR, VCD and Raman Spectra for 13C-Labeled Beta Sheets Biophysical Journal. 104: 684a. DOI: 10.1016/J.Bpj.2012.11.3779 |
0.64 |
|
| 2013 |
Chi H, Welch WR, Kubelka J, Keiderling TA. Aggregation and Fibril Formation in Oligo-Glu. Use of Isotope Edited Vibrational Spectra to Assign Structure Biophysical Journal. 104: 394a. DOI: 10.1016/J.Bpj.2012.11.2197 |
0.731 |
|
| 2012 |
Welch WR, Kubelka J. DFT-based simulations of amide I' IR spectra of a small protein in solution using empirical electrostatic map with a continuum solvent model. The Journal of Physical Chemistry. B. 116: 10739-47. PMID 22891757 DOI: 10.1021/Jp305387X |
0.424 |
|
| 2012 |
Buchner GS, Shih N, Reece AE, Niebling S, Kubelka J. Unusual cold denaturation of a small protein domain. Biochemistry. 51: 6496-8. PMID 22871296 DOI: 10.1021/Bi300916V |
0.321 |
|
| 2012 |
Buchner GS, Kubelka J. Isotope-edited infrared spectroscopy. Methods in Molecular Biology (Clifton, N.J.). 895: 347-58. PMID 22760327 DOI: 10.1007/978-1-61779-927-3_20 |
0.477 |
|
| 2012 |
Lai J, Jin J, Kubelka J, Liberles DA. A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. Journal of Molecular Biology. 422: 442-59. PMID 22651983 DOI: 10.1016/j.jmb.2012.05.028 |
0.303 |
|
| 2012 |
Buchner G, Shih N, Kubelka J. Cold Denaturation in a Small Protein Domain Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2489 |
0.349 |
|
| 2011 |
Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. Biophysical and structural considerations for protein sequence evolution. Bmc Evolutionary Biology. 11: 361. PMID 22171550 DOI: 10.1186/1471-2148-11-361 |
0.353 |
|
| 2011 |
Grahnen JA, Kubelka J, Liberles DA. Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution. Journal of Molecular Evolution. 73: 23-33. PMID 21800121 DOI: 10.1007/S00239-011-9454-3 |
0.324 |
|
| 2011 |
Kaminský J, Kubelka J, Bour P. Theoretical modeling of peptide α-helical circular dichroism in aqueous solution. The Journal of Physical Chemistry. A. 115: 1734-42. PMID 21322543 DOI: 10.1021/Jp110418W |
0.493 |
|
| 2011 |
Kaminský J, Bouř P, Kubelka J. Simulations of the temperature dependence of amide I vibration. The Journal of Physical Chemistry. A. 115: 30-4. PMID 21141980 DOI: 10.1021/Jp1084839 |
0.445 |
|
| 2011 |
Buchner GS, Murphy RD, Buchete NV, Kubelka J. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory. Biochimica Et Biophysica Acta. 1814: 1001-20. PMID 20883829 DOI: 10.1016/J.Bbapap.2010.09.013 |
0.379 |
|
| 2011 |
Buchner G, Amunson KE, Kubelka J. Folding Mechanism of a Helix-Turn-Helix Protein from Combined 13C-Edited IR and Mutational Studies Biophysical Journal. 100: 3-9. DOI: 10.1016/J.Bpj.2010.12.2373 |
0.395 |
|
| 2011 |
Grahnen J, Kubelka J. DFT-Based Simulations of Ir Amide I’ Spectra for a Small Protein in Solution Biophysical Journal. 100: 314a. DOI: 10.1016/J.Bpj.2010.12.1916 |
0.518 |
|
| 2010 |
Grahnen JA, Amunson KE, Kubelka J. DFT-based simulations of IR amide I' spectra for a small protein in solution. Comparison of explicit and empirical solvent models. The Journal of Physical Chemistry. B. 114: 13011-20. PMID 20857992 DOI: 10.1021/Jp106639S |
0.522 |
|
| 2010 |
Lai J, Amunson KE, Kubelka J. Analysis of Site-Specific Folding of Helix-Turn-Helix Proteins with Statistical-Mechanical Models Biophysical Journal. 98: 637. DOI: 10.1016/J.Bpj.2009.12.3491 |
0.404 |
|
| 2010 |
Buchner G, Amunson KE, Kubelka J. Effects of Mutations on Side-Specific Folding Mechanism of a Helix-Turn-Helix Protein Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.183 |
0.337 |
|
| 2010 |
Kubelka J, Bour P, Silva RAGD, Decatur SM, Keiderling TA. ChemInform Abstract: Chirality in Peptide Vibrations: ab initio Computational Studies of Length, Solvation, Hydrogen Bond, Dipole Coupling, and Isotope Effects on Vibrational CD. Cheminform. 33: no-no. DOI: 10.1002/chin.200239296 |
0.569 |
|
| 2009 |
Kubelka J, Bouř P. Simulation of Vibrational Spectra of Large Molecules by Arbitrary Time Propagation. Journal of Chemical Theory and Computation. 5: 200-7. PMID 26609833 DOI: 10.1021/Ct800298N |
0.41 |
|
| 2009 |
Nettels D, Müller-Späth S, Küster F, Hofmann H, Haenni D, Rüegger S, Reymond L, Hoffmann A, Kubelka J, Heinz B, Gast K, Best RB, Schuler B. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proceedings of the National Academy of Sciences of the United States of America. 106: 20740-5. PMID 19933333 DOI: 10.1073/Pnas.0900622106 |
0.374 |
|
| 2009 |
Murza A, Kubelka J. Beyond the nearest-neighbor Zimm-Bragg model for helix-coil transition in peptides. Biopolymers. 91: 120-31. PMID 18814306 DOI: 10.1002/Bip.21093 |
0.432 |
|
| 2009 |
Kubelka J, Bouř P, Keiderling TA. Quantum mechanical calculations of peptide vibrational force fields and spectral intensities Advances in Biomedical Spectroscopy. 2: 178-223. DOI: 10.3233/978-1-60750-045-2-178 |
0.614 |
|
| 2009 |
Ackels L, Stawski P, Amunson KE, Kubelka J. On the temperature dependence of amide I intensities of peptides in solution Vibrational Spectroscopy. 50: 2-9. DOI: 10.1016/J.Vibspec.2008.07.004 |
0.419 |
|
| 2008 |
Kubelka J, Henry ER, Cellmer T, Hofrichter J, Eaton WA. Chemical, physical, and theoretical kinetics of an ultrafast folding protein Proceedings of the National Academy of Sciences of the United States of America. 105: 18655-18662. PMID 19033473 DOI: 10.1073/Pnas.0808600105 |
0.366 |
|
| 2008 |
Amunson KE, Ackels L, Kubelka J. Site-specific unfolding thermodynamics of a helix-turn-helix protein. Journal of the American Chemical Society. 130: 8146-7. PMID 18529000 DOI: 10.1021/Ja802185E |
0.43 |
|
| 2008 |
Godoy-Ruiz R, Henry ER, Kubelka J, Hofrichter J, Muñoz V, Sanchez-Ruiz JM, Eaton WA. Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data Journal of Physical Chemistry B. 112: 5938-5949. PMID 18278894 DOI: 10.1021/Jp0757715 |
0.333 |
|
| 2007 |
Cellmer T, Henry ER, Kubelka J, Hofrichter J, Eaton WA. Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration Journal of the American Chemical Society. 129: 14564-14565. PMID 17983235 DOI: 10.1021/Ja0761939 |
0.305 |
|
| 2007 |
Huang R, Setnicka V, Etienne MA, Kim J, Kubelka J, Hammer RP, Keiderling TA. Cross-strand coupling of a beta-hairpin peptide stabilized with an Aib-Gly turn studied using isotope-edited IR spectroscopy. Journal of the American Chemical Society. 129: 13592-603. PMID 17929810 DOI: 10.1021/Ja0736414 |
0.717 |
|
| 2007 |
Amunson KE, Kubelka J. On the temperature dependence of amide I frequencies of peptides in solution. The Journal of Physical Chemistry. B. 111: 9993-8. PMID 17676791 DOI: 10.1021/Jp072454P |
0.414 |
|
| 2007 |
Turner DR, Kubelka J. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent. The Journal of Physical Chemistry. B. 111: 1834-45. PMID 17256894 DOI: 10.1021/Jp0666840 |
0.498 |
|
| 2006 |
Kim J, Huang R, Kubelka J, Bou Rcaron P, Keiderling TA. Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: correlation between conformational fluctuation and vibrational coupling. The Journal of Physical Chemistry. B. 110: 23590-602. PMID 17107215 DOI: 10.1021/Jp0640575 |
0.74 |
|
| 2006 |
Magg C, Kubelka J, Holtermann G, Haas E, Schmid FX. Specificity of the Initial Collapse in the Folding of the Cold Shock Protein Journal of Molecular Biology. 360: 1067-1080. PMID 16815441 DOI: 10.1016/J.Jmb.2006.05.073 |
0.389 |
|
| 2006 |
Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J. Sub-microsecond protein folding. Journal of Molecular Biology. 359: 546-53. PMID 16643946 DOI: 10.1016/J.Jmb.2006.03.034 |
0.354 |
|
| 2006 |
Kubelka J, Kim J, Bour P, Keiderling TA. Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures Vibrational Spectroscopy. 42: 63-73. DOI: 10.1016/J.Vibspec.2006.04.003 |
0.666 |
|
| 2005 |
Kubelka J, Huang R, Keiderling TA. Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water. The Journal of Physical Chemistry. B. 109: 8231-43. PMID 16851962 DOI: 10.1021/Jp0506078 |
0.724 |
|
| 2005 |
Chiu TK, Kubelka J, Herbst-Irmer R, Eaton WA, Hofrichter J, Davies DR. High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proceedings of the National Academy of Sciences of the United States of America. 102: 7517-22. PMID 15894611 DOI: 10.1073/Pnas.0502495102 |
0.347 |
|
| 2005 |
Setnicka V, Huang R, Thomas CL, Etienne MA, Kubelka J, Hammer RP, Keiderling TA. IR study of cross-strand coupling in a beta-hairpin peptide using isotopic labels. Journal of the American Chemical Society. 127: 4992-3. PMID 15810813 DOI: 10.1021/Ja043007F |
0.676 |
|
| 2005 |
Buscaglia M, Kubelka J, Eaton WA, Hofrichter J. Determination of ultrafast protein folding rates from loop formation dynamics Journal of Molecular Biology. 347: 657-664. PMID 15755457 DOI: 10.1016/J.Jmb.2005.01.057 |
0.363 |
|
| 2005 |
Keiderling TA, Huang R, Kubelka J, Bouř P, Setnička V, Hammer RP, Etienne MA, Silva RAGD, Decatur SM. Isotopically labeled peptides provide site-resolved structural data with infrared spectra. Probing the structural limit of optical spectroscopy Collection of Czechoslovak Chemical Communications. 8: 42-49. DOI: 10.1135/Css200508042 |
0.66 |
|
| 2004 |
Kubelka J, Hofrichter J, Eaton WA. The protein folding 'speed limit' Current Opinion in Structural Biology. 14: 76-88. PMID 15102453 DOI: 10.1016/J.Sbi.2004.01.013 |
0.348 |
|
| 2004 |
Huang R, Kubelka J, Barber-Armstrong W, Silva RA, Decatur SM, Keiderling TA. Nature of vibrational coupling in helical peptides: an isotopic labeling study. Journal of the American Chemical Society. 126: 2346-54. PMID 14982438 DOI: 10.1021/Ja037998T |
0.762 |
|
| 2003 |
Hilario J, Kubelka J, Keiderling TA. Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution. Journal of the American Chemical Society. 125: 7562-74. PMID 12812496 DOI: 10.1021/Ja030039E |
0.782 |
|
| 2003 |
Kubelka J, Eaton WA, Hofrichter J. Experimental tests of villin subdomain folding simulations Journal of Molecular Biology. 329: 625-630. PMID 12787664 DOI: 10.1016/S0022-2836(03)00519-9 |
0.366 |
|
| 2002 |
Silva RA, Yasui SC, Kubelka J, Formaggio F, Crisma M, Toniolo C, Keiderling TA. Discriminating 3(10)- from alpha-helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides. Biopolymers. 65: 229-43. PMID 12382284 DOI: 10.1002/Bip.10241 |
0.745 |
|
| 2002 |
Bour P, Kubelka J, Keiderling TA. Ab initio quantum mechanical models of peptide helices and their vibrational spectra. Biopolymers. 65: 45-59. PMID 12209472 DOI: 10.1002/Bip.10224 |
0.689 |
|
| 2002 |
Hilario J, Kubelka J, Syud FA, Gellman SH, Keiderling TA. Spectroscopic characterization of selected beta- sheet hairpin models. Biopolymers. 67: 233-6. PMID 12012436 DOI: 10.1002/Bip.10094 |
0.76 |
|
| 2002 |
Kubelka J, Silva RA, Keiderling TA. Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra. Journal of the American Chemical Society. 124: 5325-32. PMID 11996573 DOI: 10.1021/Ja012685O |
0.731 |
|
| 2002 |
Kubelka J, Bour P, Silva RAGD, Decatur SM, Keiderling TA. Chirality in peptide vibrations: Ab initio computational studies of length, solvation, hydrogen bond, dipole coupling, and isotope effects on vibrational CD Acs Symposium Series. 810: 50-64. |
0.569 |
|
| 2001 |
Kubelka J, Keiderling TA. Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets. Journal of the American Chemical Society. 123: 12048-58. PMID 11724613 DOI: 10.1021/Ja0116627 |
0.678 |
|
| 2001 |
Kubelka J, Keiderling TA. The anomalous infrared amide I intensity distribution in (13)C isotopically labeled peptide beta-sheets comes from extended, multiple-stranded structures: an ab initio study. Journal of the American Chemical Society. 123: 6142-50. PMID 11414848 DOI: 10.1021/Ja010270X |
0.636 |
|
| 2001 |
Kubelka J, Keiderling TA. Ab initio calculation of amide carbonyl stretch vibrational frequencies in solution with modified basis sets. 1. JV-methyl acetamide Journal of Physical Chemistry A. 105: 10922-10928. DOI: 10.1021/Jp013203Y |
0.508 |
|
| 2000 |
Silva RA, Kubelka J, Bour P, Decatur SM, Keiderling TA. Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution. Proceedings of the National Academy of Sciences of the United States of America. 97: 8318-23. PMID 10880566 DOI: 10.1073/Pnas.140161997 |
0.76 |
|
| 2000 |
Bour P, Kubelka J, Keiderling TA. Simulations of oligopeptide vibrational CD: effects of isotopic labeling. Biopolymers. 53: 380-95. PMID 10738200 DOI: 10.1002/(Sici)1097-0282(20000415)53:5<380::Aid-Bip3>3.0.Co;2-R |
0.705 |
|
| 1999 |
Kubelka J, Pancoska P, Keiderling TA. Novel use of a static modification of two-dimensional correlation analysis. Part II: Hetero-spectral correlations of protein Raman, FT-IR, and circular dichroism spectra Applied Spectroscopy. 53: 666-671. DOI: 10.1366/0003702991947315 |
0.605 |
|
| 1999 |
Pancoska P, Kubelka J, Keiderling TA. Novel use of a static modification of two-dimensional correlation analysis. Part I: Comparison of the secondary structure sensitivity of electronic circular dichroism, FT-IR, and Raman spectra of proteins Applied Spectroscopy. 53: 655-665. DOI: 10.1366/0003702991947306 |
0.609 |
|
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