Nonlinear Signal Analysis Methods in the Elucidation of Protein Sequence−Structure Relationships
- Alessandro Giuliani ,
- Romualdo Benigni ,
- Joseph P. Zbilut ,
- Charles L. Webber, ,
- Paolo Sirabella , and
- Alfredo Colosimo
Note: In lieu of an abstract, this is the article's first page.
*
To whom correspondence should be addressed. E-mail: [email protected]
†
Istituto Superiore di Sanità.
‡
Rush University.
§
Loyola University Medical Center.
‖
University of Rome.
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- A. D. Fragkou, T. E. Karakasidis, E. Nathanail. Detection of traffic incidents using nonlinear time series analysis. Chaos: An Interdisciplinary Journal of Nonlinear Science 2018, 28 (6) , 063108. https://doi.org/10.1063/1.5024924
- Lorenzo Livi, Cesare Alippi. One-Class Classifiers Based on Entropic Spanning Graphs. IEEE Transactions on Neural Networks and Learning Systems 2017, 28 (12) , 2846-2858. https://doi.org/10.1109/TNNLS.2016.2608983
- Wael I. Karain. Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method. BMC Bioinformatics 2017, 18 (1) https://doi.org/10.1186/s12859-017-1943-y
- Alessio Martino, Enrico Maiorino, Alessandro Giuliani, Mauro Giampieri, Antonello Rizzi. Supervised Approaches for Function Prediction of Proteins Contact Networks from Topological Structure Information. 2017,,, 285-296. https://doi.org/10.1007/978-3-319-59126-1_24
- . References. 2016,,, 631-694. https://doi.org/10.1016/B978-0-12-805462-8.00015-7
- Kristina N. Woods, Juergen Pfeffer. Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes. Molecular Biology and Evolution 2016, 33 (1) , 40-61. https://doi.org/10.1093/molbev/msv178
- Rinku Jacob, K. P. Harikrishnan, R. Misra, G. Ambika. Uniform framework for the recurrence-network analysis of chaotic time series. Physical Review E 2016, 93 (1) https://doi.org/10.1103/PhysRevE.93.012202
- A. D. Fragkou, T. E. Karakasidis, I. E. Sarris, A. Liakopoulos. Spatiotemporal Time Series Analysis Methods for the Study of Turbulent Magnetohydrodynamic Channel Flows. Environmental Processes 2015, 2 (S1) , 141-158. https://doi.org/10.1007/s40710-015-0095-1
- Alfredo Colosimo, Alessandro Giuliani. From Time to Space Recurrences in Biopolymers. 2015,,, 167-193. https://doi.org/10.1007/978-3-319-07155-8_5
- J.A. Schetz. Structure-Activity Relationships: Theory, Uses and Limitations☆. 2015,,https://doi.org/10.1016/B978-0-12-801238-3.05329-0
- Hiba Fataftah, Wael Karain. Detecting protein atom correlations using correlation of probability of recurrence. Proteins: Structure, Function, and Bioinformatics 2014, 82 (9) , 2180-2189. https://doi.org/10.1002/prot.24574
- E. Tejera, J. Nieto-Villar, I. Rebelo. Protein sequence complexity revisited. Relationship with fractal 3D structure, topological and kinetic parameters. Physica A: Statistical Mechanics and its Applications 2014, 410 , 287-301. https://doi.org/10.1016/j.physa.2014.05.019
- Maria Secrier, Reinhard Schneider. Visualizing time-related data in biology, a review. Briefings in Bioinformatics 2014, 15 (5) , 771-782. https://doi.org/10.1093/bib/bbt021
- K. N. Woods. Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity. Soft Matter 2014, 10 (24) , 4387. https://doi.org/10.1039/c3sm53229a
- Milan Randić, Marjana Novič, Dejan Plavšić. Milestones in graphical bioinformatics. International Journal of Quantum Chemistry 2013, 113 (22) , 2413-2446. https://doi.org/10.1002/qua.24479
- Zu-Guo Yu, Vo Anh, Jian-Yi Yang, Shao-Ming Zhu. Fractal Related Methods for Predicting Protein Structure Classes and Functions. 2013,,, 317-337. https://doi.org/10.1002/9781118567869.ch16
- S. Rackovsky. Sequence determinants of protein architecture. Proteins: Structure, Function, and Bioinformatics 2013, 81 (10) , 1681-1685. https://doi.org/10.1002/prot.24328
- Guo Sheng Han, Zu Guo Yu, Vo Anh, Anaththa P. D. Krishnajith, Yu-Chu Tian, . An Ensemble Method for Predicting Subnuclear Localizations from Primary Protein Structures. PLoS ONE 2013, 8 (2) , e57225. https://doi.org/10.1371/journal.pone.0057225
- Saritha Namboodiri, Alessandro Giuliani, Achuthsankar S. Nair, Pawan K Dhar. Looking for a sequence based allostery definition: A statistical journey at different resolution scales. Journal of Theoretical Biology 2012, 304 , 211-218. https://doi.org/10.1016/j.jtbi.2012.03.005
- NOAH C. BENSON, VALERIE DAGGETT. WAVELET ANALYSIS OF PROTEIN MOTION. International Journal of Wavelets, Multiresolution and Information Processing 2012, 10 (04) , 1250040. https://doi.org/10.1142/S0219691312500403
- Xiaojuan Shen. Symmetry Recurrence in protein sequence and structure with Pearson's correlation coefficients. 2012,,, 832-835. https://doi.org/10.1109/BHI.2012.6211714
- Giovanna Zimatore, Marta Cavagnaro, Alessandro Giuliani, Alfredo Colosimo. Reproducing Cochlear Signals by a Minimal Electroacoustic Model. Open Journal of Biophysics 2012, 02 (02) , 33-39. https://doi.org/10.4236/ojbiphy.2012.22005
- Guo-Sheng Han, Zu-Guo Yu, Anh Vo. Predicting the subcellular location of apoptosis proteins based on recurrence quantification analysis and the Hilbert—Huang transform. Chinese Physics B 2011, 20 (10) , 100504. https://doi.org/10.1088/1674-1056/20/10/100504
- Xiaojuan Shen. Conformation and sequence evidence for two-fold symmetry in left-handed beta-helix fold. Journal of Theoretical Biology 2011, 285 (1) , 77-83. https://doi.org/10.1016/j.jtbi.2011.06.011
- Xiaofeng Ji, Jun Sheng, Fang Wang, Suzhen Zhang, Jianhua Hao, Haiying Wang, Mi Sun. Identification of latent periodicity in domains of alkaline proteases. Biochemistry (Moscow) 2011, 76 (9) , 1037-1042. https://doi.org/10.1134/S0006297911090082
- Rui Zhou, Yi He, Yi Xiao. Multi-nucleation and vectorial folding pathways of large helix protein. Computational Biology and Chemistry 2011, 35 (3) , 169-173. https://doi.org/10.1016/j.compbiolchem.2011.04.004
- S. Rackovsky. Spectral Analysis of a Protein Conformational Switch. Physical Review Letters 2011, 106 (24) https://doi.org/10.1103/PhysRevLett.106.248101
- ABHIJIT KULKARNI, SHREYAS KARNIK, SAVITA ANGADI. ANALYSIS OF INTRINSICALLY DISORDERED REGIONS IN PROTEINS USING RECURRENCE QUANTIFICATION ANALYSIS. International Journal of Bifurcation and Chaos 2011, 21 (04) , 1193-1202. https://doi.org/10.1142/S0218127411028969
- REIK V. DONNER, MICHAEL SMALL, JONATHAN F. DONGES, NORBERT MARWAN, YONG ZOU, RUOXI XIANG, JÜRGEN KURTHS. RECURRENCE-BASED TIME SERIES ANALYSIS BY MEANS OF COMPLEX NETWORK METHODS. International Journal of Bifurcation and Chaos 2011, 21 (04) , 1019-1046. https://doi.org/10.1142/S0218127411029021
- Xiaofeng Ji, Haiying Wang, Jianhua Hao, Yuan Zheng, Wei Wang, Mi Sun. Identification of sequence repetitions in immunoglobulin folds. Journal of Molecular Graphics and Modelling 2010, 28 (8) , 788-791. https://doi.org/10.1016/j.jmgm.2010.02.003
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- S. Rackovsky. Global characteristics of protein sequences and their implications. Proceedings of the National Academy of Sciences 2010, 107 (19) , 8623-8626. https://doi.org/10.1073/pnas.1001299107
- Norbert Marwan, Jonathan F. Donges, Yong Zou, Reik V. Donner, Jürgen Kurths. Complex network approach for recurrence analysis of time series. Physics Letters A 2009, 373 (46) , 4246-4254. https://doi.org/10.1016/j.physleta.2009.09.042
- Charles L. Webber, Norbert Marwan, Angelo Facchini, Alessandro Giuliani. Simpler methods do it better: Success of Recurrence Quantification Analysis as a general purpose data analysis tool. Physics Letters A 2009, 373 (41) , 3753-3756. https://doi.org/10.1016/j.physleta.2009.08.052
- Joseph P. Zbilut. Biosignatures of Health. Biological Research For Nursing 2009, 11 (2) , 208-220. https://doi.org/10.1177/1099800409341176
- Yi He, Rui Zhou, Yanzhao Huang, Yi Xiao. Foldable subunits of helix protein. Computational Biology and Chemistry 2009, 33 (4) , 325-328. https://doi.org/10.1016/j.compbiolchem.2009.06.001
- T. E. KARAKASIDIS, A. LIAKOPOULOS, A. FRAGKOU, P. PAPANICOLAOU. RECURRENCE QUANTIFICATION ANALYSIS OF TEMPERATURE FLUCTUATIONS IN A HORIZONTAL ROUND HEATED TURBULENT JET. International Journal of Bifurcation and Chaos 2009, 19 (08) , 2487-2498. https://doi.org/10.1142/S0218127409024268
- Jian-Yi Yang, Zu-Guo Yu, Vo Anh. Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids. Chaos, Solitons & Fractals 2009, 40 (2) , 607-620. https://doi.org/10.1016/j.chaos.2007.08.014
- Jian-Yi Yang, Zhen-Ling Peng, Zu-Guo Yu, Rui-Jie Zhang, Vo Anh, Desheng Wang. Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation. Journal of Theoretical Biology 2009, 257 (4) , 618-626. https://doi.org/10.1016/j.jtbi.2008.12.027
- N. Marwan. A historical review of recurrence plots. The European Physical Journal Special Topics 2008, 164 (1) , 3-12. https://doi.org/10.1140/epjst/e2008-00829-1
- Yuchen Yang, Erwin Tantoso, Kuo-Bin Li. Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. Journal of Theoretical Biology 2008, 252 (1) , 145-154. https://doi.org/10.1016/j.jtbi.2008.01.028
- Yu Zhou, Zu-Guo Yu, Vo Anh. Protein Structure Classification Using Local Holder Exponents Estimated by Wavelet Transform. 2008,,, 104-108. https://doi.org/10.1109/ICNC.2008.296
- L. Ye, Z. Wu, M. Eleftheriou, R. Zhou. Single-mutation-induced stability loss in protein lysozyme. Biochemical Society Transactions 2007, 35 (6) , 1551-1557. https://doi.org/10.1042/BST0351551
- Yu Zhou, Zu-Guo Yu, Vo Anh. Cluster protein structures using recurrence quantification analysis on coordinates of alpha-carbon atoms of proteins. Physics Letters A 2007, 368 (3-4) , 314-319. https://doi.org/10.1016/j.physleta.2007.04.012
- T. E. Karakasidis, A. Fragkou, A. Liakopoulos. System dynamics revealed by recurrence quantification analysis: Application to molecular dynamics simulations. Physical Review E 2007, 76 (2) https://doi.org/10.1103/PhysRevE.76.021120
- Yanzhao Huang, Yi Xiao. Detection of gene duplication signals of Ig folds from their amino acid sequences. Proteins: Structure, Function, and Bioinformatics 2007, 68 (1) , 267-272. https://doi.org/10.1002/prot.21330
- Miika Ahdesmaki, Janita Thusberg, Heikki Huttunen, Mauno Vihinen, Olli Yli-Harja. Detection of Pathogenic Mutation Prone Locations from Protein Sequences using Solvent Accessibility Measurements. 2007,,, 1-4. https://doi.org/10.1109/GENSIPS.2007.4365845
- Karen A. Selz, Tatiana I. Samoylova, Alexandre M. Samoylov, Vitaly J. Vodyanoy, Arnold J. Mandell. Designing allosteric peptide ligands targeting a globular protein. Biopolymers 2007, 85 (1) , 38-59. https://doi.org/10.1002/bip.20607
- A. Tropsha. Predictive Quantitative Structure–Activity Relationship Modeling. 2007,,, 149-165. https://doi.org/10.1016/B0-08-045044-X/00248-0
- John A. Schetz. Structure-Activity Relationships. 2007,,, 1-12. https://doi.org/10.1016/B978-008055232-3.60006-6
- Joseph P. Zbilut, Charles L. Webber. Recurrence Quantification Analysis. 2006,,https://doi.org/10.1002/9780471740360.ebs1355
- Franco Orsucci, Alessandro Giuliani, Charles Webber, Joseph Zbilut, Peter Fonagy, Marianna Mazza. Combinatorics and synchronization in natural semiotics. Physica A: Statistical Mechanics and its Applications 2006, 361 (2) , 665-676. https://doi.org/10.1016/j.physa.2005.06.044
- Véronique Receveur-Bréchot, Jean-Marie Bourhis, Vladimir N. Uversky, Bruno Canard, Sonia Longhi. Assessing protein disorder and induced folding. Proteins: Structure, Function, and Bioinformatics 2006, 62 (1) , 24-45. https://doi.org/10.1002/prot.20750
- Mauro Colafranceschi, Massimiliano Papi, Alessandro Giuliani, Gino Amiconi, Alfredo Colosimo. Simulated Point Mutations in the Aα-Chain of Human Fibrinogen Support a Role of the αC Domain in the Stabilization of Fibrin Gel. Pathophysiology of Haemostasis and Thrombosis 2006, 35 (6) , 417-427. https://doi.org/10.1159/000102048
- LEI YE, HUAJUN CHEN, TING LIU, ZHAOHUI WU, JINGYUAN LI, RUHONG ZHOU. A WAVELET APPROACH FOR THE ANALYSIS OF FOLDING TRAJECTORY OF PROTEIN TRP-CAGE. Journal of Bioinformatics and Computational Biology 2005, 03 (06) , 1351-1370. https://doi.org/10.1142/S0219720005001594
- Joseph P. Zbilut, Thomas Scheibel, Daniel Huemmerich, Charles L. Webber, Mauro Colafranceschi, Alessandro Giuliani. Spatial stochastic resonance in protein hydrophobicity. Physics Letters A 2005, 346 (1-3) , 33-41. https://doi.org/10.1016/j.physleta.2005.07.072
- Nooshin Alizadeh-Pasdar, Shuryo Nakai. Rational Designing of Bioactive Peptides. 2005,,, 565-582. https://doi.org/10.1201/9781420028836.ch28
- E. Cazares-Ibáñez, G.A. Vázquez-Coutiño, E. García-Ochoa. Application of recurrence plots as a new tool in the analysis of electrochemical oscillations of copper. Journal of Electroanalytical Chemistry 2005, 583 (1) , 17-33. https://doi.org/10.1016/j.jelechem.2005.03.046
- Ruizhen Xu, Yi Xiao. A common sequence-associated physicochemical feature for proteins of beta-trefoil family. Computational Biology and Chemistry 2005, 29 (1) , 79-82. https://doi.org/10.1016/j.compbiolchem.2004.12.003
- Madhavi Ganapathiraju, Narayanas Balakrishnan, Raj Reddy, Judith Klein-Seetharaman. Computational Biology and Language. 2005,,, 25-47. https://doi.org/10.1007/978-3-540-32263-4_2
- Joseph P. Zbilut, Julie C. Mitchell, Alessandro Giuliani, Alfredo Colosimo, Norbert Marwan, Charles L. Webber. Singular hydrophobicity patterns and net charge: a mesoscopic principle for protein aggregation/folding. Physica A: Statistical Mechanics and its Applications 2004, 343 , 348-358. https://doi.org/10.1016/j.physa.2004.05.081
- In-Ho Song, Doo-Soo Lee, Sun I Kim. Recurrence quantification analysis of sleep electoencephalogram in sleep apnea syndrome in humans. Neuroscience Letters 2004, 366 (2) , 148-153. https://doi.org/10.1016/j.neulet.2004.05.025
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- Karen A. Selz, Arnold J. Mandell, Michael F. Shlesinger, Vani Arcuragi, Michael J. Owens. Designing Human m1 Muscarinic Receptor-Targeted Hydrophobic Eigenmode Matched Peptides as Functional Modulators. Biophysical Journal 2004, 86 (3) , 1308-1331. https://doi.org/10.1016/S0006-3495(04)74204-6
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- . Bibliography. 2004,,, 221-230. https://doi.org/10.1016/B978-044451613-8/50009-9
- S. Nakai. Modelling protein behaviour. 2004,,, 245-269. https://doi.org/10.1533/9781855738379.2.245
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- Yi Xiao, Yanzhao Huang, Mingfeng Li, Ruizhen Xu, Saifeng Xiao. Nonlinear analysis of correlations in Alu repeat sequences in DNA. Physical Review E 2003, 68 (6) https://doi.org/10.1103/PhysRevE.68.061913
- A. Colosimo, A. Giuliani, F. Maranghi, O. Brix, S. Thorkildsen, T. Fischer, R. Knust, H.O. Poertner. Physiological and genetical adaptation to temperature in fish populations. Continental Shelf Research 2003, 23 (17-19) , 1919-1928. https://doi.org/10.1016/j.csr.2003.06.012
- Shuryo Nakai. Measurement of Protein Hydrophobicity. Current Protocols in Food Analytical Chemistry 2003, 9 (1) https://doi.org/10.1002/0471142913.fab0502s09
- Arnold J Mandell, Karen A Selz, Michael J Owens, Becky Kinkead, Michael F Shlesinger, David A Gutman, Vani Arguragi. Cellular and Behavioral Effects of D2 Dopamine Receptor Hydrophobic Eigenmode-Targeted Peptide Ligands. Neuropsychopharmacology 2003, 28 (S1) , S98-S107. https://doi.org/10.1038/sj.npp.1300134
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- Alessandro Giuliani, Romualdo Benigni, Joseph P. Zbilut, Charles L. Webber Jr., Paolo Sirabella, Alfredo Colosimo. ChemInform Abstract: Nonlinear Signal Analysis Methods in the Elucidation of Protein Sequence-Structure Relationships. ChemInform 2002, 33 (28) , no-no. https://doi.org/10.1002/chin.200228300



