Tobin R. Sosnick to Models, Molecular
This is a "connection" page, showing publications Tobin R. Sosnick has written about Models, Molecular.
Connection Strength
4.712
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Factors that control the chemistry of the LOV domain photocycle. PLoS One. 2014; 9(1):e87074.
Score: 0.348
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Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein. Biophys J. 2013 Aug 20; 105(4):1027-36.
Score: 0.337
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Protein vivisection reveals elusive intermediates in folding. J Mol Biol. 2010 Apr 02; 397(3):777-88.
Score: 0.264
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Psi-constrained simulations of protein folding transition states: implications for calculating. J Mol Biol. 2009 Mar 06; 386(4):920-8.
Score: 0.248
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Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci U S A. 2008 Aug 05; 105(31):10709-14.
Score: 0.237
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Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys. 2007 May; 40(2):113-61.
Score: 0.225
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Characterizing protein folding transition States using Psi-analysis. Methods Mol Biol. 2007; 350:83-104.
Score: 0.213
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Characterizing the protein folding transition state using psi analysis. Chem Rev. 2006 May; 106(5):1862-76.
Score: 0.203
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RNA folding: models and perspectives. Curr Opin Struct Biol. 2003 Jun; 13(3):309-16.
Score: 0.166
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Distinguishing between two-state and three-state models for ubiquitin folding. Biochemistry. 2000 Sep 26; 39(38):11696-701.
Score: 0.138
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Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different. J Mol Biol. 2020 04 17; 432(9):2882-2889.
Score: 0.132
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Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. PLoS Comput Biol. 2018 12; 14(12):e1006342.
Score: 0.122
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Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange. Proc Natl Acad Sci U S A. 2016 Apr 26; 113(17):4747-52.
Score: 0.101
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Folding of a large protein at high structural resolution. Proc Natl Acad Sci U S A. 2013 Nov 19; 110(47):18898-903.
Score: 0.086
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A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable. Protein Sci. 2012 Jun; 21(6):819-27.
Score: 0.077
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The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized). J Mol Biol. 2012 Jul 13; 420(3):220-34.
Score: 0.077
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The amino-terminal helix modulates light-activated conformational changes in AsLOV2. J Mol Biol. 2012 May 25; 419(1-2):61-74.
Score: 0.076
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Modeling large regions in proteins: applications to loops, termini, and folding. Protein Sci. 2012 Jan; 21(1):107-21.
Score: 0.075
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The folding of single domain proteins--have we reached a consensus? Curr Opin Struct Biol. 2011 Feb; 21(1):12-24.
Score: 0.070
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Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. J Am Chem Soc. 2010 Nov 24; 132(46):16352-3.
Score: 0.069
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A probabilistic and continuous model of protein conformational space for template-free modeling. J Comput Biol. 2010 Jun; 17(6):783-98.
Score: 0.067
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Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates. Biochemistry. 2009 Apr 07; 48(13):2950-9.
Score: 0.062
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Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9.
Score: 0.062
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Quantifying the structural requirements of the folding transition state of protein A and other systems. J Mol Biol. 2008 Sep 19; 381(5):1362-81.
Score: 0.059
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Kinetic barriers and the role of topology in protein and RNA folding. Protein Sci. 2008 Aug; 17(8):1308-18.
Score: 0.059
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Methods for the accurate estimation of confidence intervals on protein folding phi-values. Protein Sci. 2006 Oct; 15(10):2257-64.
Score: 0.052
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Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol. 2006 Nov 03; 363(4):835-57.
Score: 0.052
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Small proteins fold through transition states with native-like topologies. J Mol Biol. 2006 Aug 25; 361(4):755-70.
Score: 0.051
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RNA folding during transcription. Annu Rev Biophys Biomol Struct. 2006; 35:161-75.
Score: 0.050
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Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol. 2005 Sep 23; 352(3):712-22.
Score: 0.049
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Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc Natl Acad Sci U S A. 2005 Sep 13; 102(37):13099-104.
Score: 0.048
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Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc Natl Acad Sci U S A. 2004 Dec 14; 101(50):17377-82.
Score: 0.046
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Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding. Proc Natl Acad Sci U S A. 2004 Nov 02; 101(44):15639-44.
Score: 0.046
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Reduced contact order and RNA folding rates. J Mol Biol. 2004 Oct 01; 342(5):1359-65.
Score: 0.046
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Fast folding of a helical protein initiated by the collision of unstructured chains. Proc Natl Acad Sci U S A. 2004 Sep 14; 101(37):13478-82.
Score: 0.045
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Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J Mol Biol. 2004 Mar 19; 337(2):463-75.
Score: 0.044
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Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. J Mol Biol. 2003 Aug 15; 331(3):693-711.
Score: 0.042
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Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol. 2002 Nov 22; 324(2):359-71.
Score: 0.040
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Dynamics of hydrogen bond desolvation in protein folding. J Mol Biol. 2002 Aug 23; 321(4):659-75.
Score: 0.039
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Entropic benefit of a cross-link in protein association. Proteins. 2002 Aug 01; 48(2):341-51.
Score: 0.039
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Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nat Struct Biol. 2002 Jun; 9(6):458-63.
Score: 0.039
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Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. Proc Natl Acad Sci U S A. 2022 01 04; 119(1).
Score: 0.038
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Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nat Struct Biol. 2001 Dec; 8(12):1042-7.
Score: 0.037
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Structural basis for adhesion G protein-coupled receptor Gpr126 function. Nat Commun. 2020 01 10; 11(1):194.
Score: 0.033
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D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding. Nat Struct Biol. 2000 Jan; 7(1):62-71.
Score: 0.033
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Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core. Proc Natl Acad Sci U S A. 2017 02 28; 114(9):2241-2246.
Score: 0.027
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Introduction of a polar core into the de novo designed protein Top7. Protein Sci. 2016 07; 25(7):1299-307.
Score: 0.025
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Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions. Proc Natl Acad Sci U S A. 2015 May 26; 112(21):6631-6.
Score: 0.024
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TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nat Methods. 2012 Mar 04; 9(4):379-84.
Score: 0.019
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Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci U S A. 2012 Feb 28; 109(9):3323-8.
Score: 0.019
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Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state. J Mol Biol. 2012 May 04; 418(3-4):226-36.
Score: 0.019
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Automated real-space refinement of protein structures using a realistic backbone move set. Biophys J. 2011 Aug 17; 101(4):899-909.
Score: 0.018
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Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2559-64.
Score: 0.015
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Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):17995-8000.
Score: 0.014
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The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell. 2007 Feb 09; 128(3):613-24.
Score: 0.013
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Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors. Biochemistry. 2007 Jan 23; 46(3):669-82.
Score: 0.013
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PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV. Proteins. 2006 May 01; 63(2):312-21.
Score: 0.013
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Stepwise conversion of a mesophilic to a thermophilic ribozyme. J Mol Biol. 2003 Jul 04; 330(2):177-83.
Score: 0.010
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Large-scale context in protein folding: villin headpiece. Biochemistry. 2003 Jan 28; 42(3):664-71.
Score: 0.010
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Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry. 2001 Sep 18; 40(37):11202-10.
Score: 0.009
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The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA. 2001 Feb; 7(2):233-41.
Score: 0.009
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Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends. Biochemistry. 1997 May 13; 36(19):5806-16.
Score: 0.007
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Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study. J Mol Biol. 1995 Jun 09; 249(3):576-94.
Score: 0.006