Computational Biophysics Group
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Publications
   
 

Selected Papers:

 

Burger VM., Vandervelde A., Hendrix J., Konijnenberg A., Sobott F., Lorisand R., Stultz CM.,  Hidden States with Disordered Regions of the CcdA Antitoxin Protein.  Journal of the American Chemical Society, in press

 

Liu Y., Scirica B.M., Stultz CM.*, Guttag JV. Beatquency domain and machine learning improve prediction of cardiovascular death after acute coronary syndrome. Nature Scientific Reports 6, Article Number 34540, 2016

Burger V., Arenas D., Stultz CM. A Structure-free Method for Quantifying Conformational Flexibility in proteins. Scientific Reports 6, Article Number 29040, 2016.

Ziegler Z., Schmidt M., Gurry T., Burger V., Stultz CM., Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins. Bioinformatics first published online April 19, 2016 doi:10.1093/bioinformatics/btw200

Burger V., Nolasco D., Stultz CM., Expanding the Range of Protein Function at the Far end of the Order-Structure Continuum.  Journal of Biological ChemistryJ. Biol. Chem. 2016 291:6706-.doi:10.1074/jbc.R115.692590

Liu Y., Chuang K., Liang F., Su H., Stultz CM, Guttag JV., Leveraging Feature Hierarchy and Bootstrap Lasso to Reduce Dimensionality and Improve Interpretability”. NIPS 2015 Workshop on Machine Learning in Healthcare

Gurry T, Fisher CK, Schmidt M, Stultz CM. Analyzing Ensembles of Amyloid Proteins Using Bayesian Statistics. Methods Mol Biol. 2016;1345:269-80. doi:10.1007/978-1-4939-2978-8_17. PubMed PMID: 26453218.

Gurry T., Stultz CM. The Mechanism of Amyloid-Beta Fibril Elongation.  Biochemistry 53, 6981−6991, DOI: 10.1021/bi500695g, 2014

Burger VM., Gurry T., Stultz CM. Intrinsically Disordered Proteins: Where Computation Meets Experiment.  Polymers 6(10) 2684-2719, 2014

Zhong C., Gurry T., Cheng Al., Downey J., Deng Z., Stultz CM., Lu TK., Biologically Inspired Engineering of Strong, Self-Assembling, and Multi-Functional Underwater Adhesives.   Nature Nanotechnology  9, 858–866,  2014

Linder D., Gurry T., Stultz CM. Towards a Consensus in Protein Structure Nomenclature. in Intrinsically Disordered Proteins. 2014 (Comment)

Yun L., Syed Z., Scirica BM, Morrow DA, Guttag JV, Stultz CM. ECG Morphological Variability in Beat-space for Risk Stratification after Acute Coronary Syndrome. Journal of the American Heart Association, 2014;3:e000981 doi:10.1161/JAHA.114.000981

Gee PS., Yuksel D., Stultz CM., Ingber DE. SLLISWD Sequence in the 10FNIII Domain Initiates Fibronectin Fibrillogenesis. Journal of Biological Chemistry 288: 21329-21340, 2013.

Lu KG., Stultz CM., Insight into the Degradation of Type-I Collagen Fibrils by MMP-8. Journal of Molecular Biology 425(10): 1815-1825, 2013.

Fisher C., Ullman O., Stultz CM., Comparative Studies of Disordered Proteins with Similar Sequences: Application to AB40 and AB42. Biophysical Journal 104: 1546-1555, 2013.

Gurry T., Ullman O., Fisher C., Perovic I., Pochapsky T., Stultz CM., The dynamic structure of alpha-synuclein multimers. Journal of the American Chemical Society 135: 3865-3872, 2013.

Liu J., Schubert C., Xiaoqin F., Houdusse A., Fourniel F., Stultz CM., Moores C., Walsh, C. Molecular Basis for Specific Regulation of Neuronal Kinesin-3 Motors by Doublecortin Family Proteins.  Molecular Cell 47: 707-721, 2012

Walker S., Ullman O., Stultz CM. Using Intramolecular Disulfide Bonds in Tau Protein to Deduce Structural Features of Aggregation-resistant Conformations. Journal of Biological Chemistry, 287(12):9591-9600, 2012

Fisher CK., Ullman O., Stultz CM.  Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations.  Pacific Symposium on Biocomputing 17:82-93, 2012

Ullman O., Fisher C., Stultz CM. Explaining the Structural Plasticity of α-Synuclein. Journal of the American Chemical Society 133 (48), 19536–19546, 2011

Syed Z., Stultz CM., Scirica BM., Guttag JV. Computationally Generated Cardiac Biomarkers for Risk Stratification Following Acute Coronary Syndrome.  Science: Translational Medicine 28 September Vol 3 Issue 102 102ra95, 2011.

Fisher CK., Stultz CM. Protein Structure along the order-disorder continuum. Journal of the American Chemical Society. 133 (26): 10022–10025, 2011.

Fisher CK., Stultz CM. Constructing Ensembles for Intrinsically Disordered Proteins. Current Opinion in Structural Biology. 21:426-431, 2011.

Chen MM., Bartlett AI., Nerenberg PS., Friel CT., Hackenberger CPR., Stultz CM., Radford SE., Imperiali B. Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation. Proceedings of the National Academy of Sciences 107 (52) 22528-22533, 2010.

Fisher CK., Huang A., Stultz CM. Modeling Intrinsically Disordered Proteins with Bayesian Statistics. Journal of the American Chemical Society 132, 14919-14927, 2010.

Phillips C., Schreiter E., Stultz CM., Drennan C. Structural Basis of Low Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli.  Biochemistry 49, 7830-7838, 2010.

Phillips C., Stultz CM., Drennan C. Searching for the nik operon: how a ligand-responsive transcription factor hunts for its DNA binding site. Biochemistry 49, 7757-7763, 2010.

Gurry T., Nerenberg P., Stultz CM. The Contribution of Inter-chain Salt Bridges to Triple Helical Stability in Collagen. Biophysical Journal 98(11) pp. 2634-2643, 2010.

Salsas-Escat R., Nerenberg P., Stultz CM. Cleavage site specificity and conformational selection in type I collagen degradation. Biochemistry, 49, 4147–4158, 2010.

Salsas-Esat R., Stultz CM., Conformational Selection and Collagenolysis in Type III Collagen. Proteins: Structure, Function, and Bioinformatics 78, 325-335 (DOI 10.1002/prot.22545), 2010

Syed Z., Stultz CM., Kellis M., Indyk P. Guttag J. Motif Discovery in Physiological Datasets: A Methodology for Inferring Predictive Elements. ACM Transactions on Knowledge Discovery from Data 4(1), Article 2, 1-23, 2010.

Phillips C., Nerenberg P., Drennan C., Stultz CM. The Physical Basis of Metal Binding Specificity in E. coli NikR. Journal of the American Chemical Society 131(29), 10220-10228 (DOI: 10.1021/ja9026314), 2009.

Schubert C., Stultz CM. The Multi-Copy Simultaneous Search Methodology: A Fundamental Tool for Structure-Based Drug Design. Journal of Computer Aided Molecular Design (DOI 10.1007/s10822-009-9287-y), 2009.

Huang A., Stultz CM. Finding Order within Disorder: Elucidating the Structure of Proteins Associated with Neurodegenerative Disease. Future Medicinal Chemistry 1(3):467-482, 2009.

Syed Z., Sung P., Sciric BM., Morrow, DA.  Stultz CM., Guttag JV. Spectral Energy of ECG Morphologic Differences to Predict Death.  Cardiovascular Engineering (DOI 10.1007/s10558-009-9066-3), 2009.

Yoon M., Venkatachalam V., Huang A., Choi B., Stultz CM., Chou JJ. Residual structure within the disordered C-terminal segment of p21Waf1/Cip1/Sdi1 and its implications for molecular recognition. Protein Science 18(2):337-347, 2009.

Syed S.., Scirica BM., Mohanavelu S., Sung P., Cannon CP., Stone PH., Stultz CM., Guttag JG. Relation of Death Within 90 Days of Non-ST-Elevation Acute Coronary Syndromes to Variability in Electrocardiographic Morphology. American Journal of Cardiology, 103(3):307-311 (DOI: 10.1016/j.amjcard.2008.09.099), 2009.

Huang A., Stultz CM. The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule Binding Repeat in Tau. PLoS Computational Biology4(8): e1000155 doi:10.1371/journal.pcbi.1000155 .

Nerenberg P., Stultz CM. Differential Unfolding of α1 and α2 chains in Type I Collagen and Collagenolysis. JMB 382, 246-256, 2008.

Gee PS. Gee, Ingber DE., Stultz CM. Fibronectin Unfolding Revisited: Modeling Cell Traction-mediated Unfolding of the Tenth Type-III Repeat Running Title: Fibronectin Unfolding Revisited.  PLoS ONE, 3(6): e2373. doi:10.1371/journal.pone.0002373.

Nerenberg P., Salsas-Escat R., Stultz CM. Do collagenases unwind triple-helical collagen prior to peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models. Proteins: Structure, Function, and Bioinformatics, 70: 1154-1161, 2008.

Nerenberg P., Salsas-Escat R., Stultz CM. Collagen – A Necessary Accomplice in the Metastatic Process. Cancer Genomics & Proteomics 4: 319-328 (2007).

Salsas-Escat R., Stultz CM. The Molecular Mechanics of Collagen Degradation:  Implications for Human Disease. Experimental Mechanics (Published online ahead of print DOI10.1007/s11340-007-9105-1).

Syed Z., Guttag J., and Stultz CM. Clustering and Symbolic Analysis of Cardiovascular Signals: Discovery and Visualization of Medically Relevant Patterns in Long-Term Data Using Limited Prior Knowledge. 2007; EURASIP Journal on Advances in Signal Processing, vol. 2007, Article ID 67938, 16 pages.

Thomas A., Edelman ER., Stultz CM. Collagen Fragments Modulate Innate Immunity. 2007; Exp. Biol. & Med. 232: 406-411

Huang, A. & Stultz CM. Conformational Sampling with Implicit Solvent Models: Application to the PHF6 Peptide in Tau Protein. 2007; Biophys. J.  92: 34–45.

Stultz, CM. The Folding Mechanism of Collagen-like Model Peptides Explored through Detailed Simulations. Protein Science. 2006; 15: 2166-2177.

Stultz CM. Cosmology and proteins: landscape of possibilities.  Nature Physics. 2006; 2(6): 357.

Stultz CM., Karplus M. In Fragment-based Approaches in Drug Discovery. Methods and Principles in Medicinal Chemistry v34. eds. Jahnke and Erlanson, Wiley-VCH, Weinheim. 2006. pg. 125-148.

Stultz CM. An Assessment of Potential of Mean Force Calculations with Implicit Solvent Models. J. Chem. Phys B. 2004; 108:16525-16532. 

Stultz CM, Edelman ER. A Structural Model that Explains the Effects of Hyperglycemia on Collagenolysis. Biophys. J. 2003; 85:2198-2204. 

Stultz CM. Localized Unfolding of Collagen Explains Collagenase Cleavage Near Imino-Poor Sites. J. Mol. Biol. 2002;319:997-1003. 

Stultz CM, Levin AD, Edelman ER. Phosphorylation Induced Conformational Changes in a MAP-Kinase Substrate: Implications for Tyrosine Hydroxylase Activation. J. Biol. Chem. 2002;277:47653-47661.

Stultz CM, Karplus M. Dynamic Ligand Design and Combinatorial Optimization. Proteins, Structure Function and Genetics. 2000; 40: 259-289. 

Stultz CM, Karplus M. MCSS Functionality Maps for a Flexible Protein. Proteins, Structure Function and Genetics. 1999;37:512-529. 

Stultz CM, Karplus M. On the Potential Surface of the Locally Enhanced Sampling Approximation. Journal of Chemical Physics. 1998; 109: 8809-8815. 

Stultz CM, Nambudripad R, Lathrop R, White JV. Predicting Protein Structure with Probabilistic Models. In: Protein Structural Biology in Bio-Medical Research , Vol. 22B of Advances in Molecular and Cell Biology series editor: E. E. Bittar, Guest Editors: N.M. Allewell and C. Woodward.  Greenwich CT: JAI Press ;1997. p. 447-506.

White JV, Stultz CM, Smith TF. Protein Classification by Stochastic Modeling and Optimal Filtering of Amino-Acid Sequences. Mathematical Biosciences. 1994; 119: 35-75. 

Stultz CM, White JV, Smith TF. Structural Analysis Based on State Space Modeling. Protein Science. 1993; 2: 305-314. 

 

 
   
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