References
- Alva, V., Söding, J., & Lupas, A. N. (2015). A vocabulary of ancient peptides at the origin of folded proteins. eLife, 4, e09410. https://doi.org/10.7554/eLife.09410
- Berezovsky, I. N., Grosberg, A. Y., & Trifonov, E. N. (2000). Closed loops of nearly standard size: Common basic element of protein structure. FEBS Letters, 466(2–3), 283–286. https://doi.org/10.1016/S0014-5793(00)01091-7 doi:10.1016/S0014-5793(00)01091-7
- Bhaskara, R. M., Brevern, A. G. D., & Srinivasan, N. (2013). Understanding the role of domain–domain linkers in the spatial orientation of domains in multi-domain proteins. Journal of Biomolecular Structure and Dynamics, 31(12), 1467–1480. https://doi.org/10.1080/07391102.2012.743438 doi:10.1080/07391102.2012.743438
- Chintapalli, S. V., Yew, B. K., Illingworth, C. J. R., Upton, G. J. G., Reeves, P. J., Parkes, K. E. B., … Reynolds, C. A. (2010). Closed loop folding units from structural alignments: Experimental foldons revisited. Journal of Computational Chemistry, 31(15), 2689–2701. https://doi.org/10.1002/jcc.21562 doi:10.1002/jcc.21562
- Ittah, V., & Haas, E. (1995). Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. Biochemistry, 34(13), 4493–4506. doi:10.1021/bi00013a042
- Koczyk, G., & Berezovsky, I. N. (2008). Domain hierarchy and closed loops (DHcL): A server for exploring hierarchy of protein domain structure. Nucleic Acids Research, 36(suppl_2), W239–W245. https://doi.org/10.1093/nar/gkn326 doi:10.1093/nar/gkn326
- Kogan, S., Frenkel, Z., Kupervasser, O., & Volkovich, Z. (2013). Hierarchy of protein loop-lock structures: A new server for the decomposition of a protein structure into a set of closed loops, 3(1):1–8. https://doi.org/10.4236/cmb.2013.31001 doi:10.4236/cmb.2013.31001
- Krishna, M. M. G., & Englander, S. W. (2005). The N-terminal to C-terminal motif in protein folding and function. Proceedings of the National Academy of Sciences, 102(4), 1053–1058. https://doi.org/10.1073/pnas.0409114102 doi:10.1073/pnas.0409114102
- Lamarine, M., Mornon, J.-P., Berezovsky, I. N., & Chomilier, J. (2001). Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: Towards an efficient punctuation of protein folding?. Cellular and Molecular Life Sciences CMLS, 58(3), 492–498. https://doi.org/10.1007/PL00000873 doi:10.1007/PL00000873
- Nepomnyachiy, S., Ben-Tal, N., & Kolodny, R. (2017). Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths. Proceedings of the National Academy of Sciences United States of America, 114(44):11703–11708. https://doi.org/10.1073/pnas.1707642114
- Postic, G., Ghouzam, Y., Chebrek, R., & Gelly, J.-C. (2017). An ambiguity principle for assigning protein structural domains. Science Advances, 3(1), e1600552. https://doi.org/10.1126/sciadv.1600552 doi:10.1126/sciadv.1600552
- Sedgewick, R. (2002). Algorithms in C++ part 5: Graph algorithms (3rd ed.). Boston, MA: Addison-Wesley Professional.
- Wang, G., & Dunbrack, R. L. (2003). PISCES: A protein sequence culling server. Bioinformatics, 19(12), 1589–1591. https://doi.org/10.1093/bioinformatics/btg224 doi:10.1093/bioinformatics/btg224
- Wetlaufer, D. B. (1973). Nucleation, rapid folding, and globular intrachain regions in proteins. Proceedings of the National Academy of Sciences, 70(3), 697–701. https://doi.org/10.1073/pnas.70.3.697 doi:10.1073/pnas.70.3.697
- Yew, B. K., Chintapalli, S. V., Upton, G. G. C., & Reynolds, C. A. (2007). Conservation of closed loops. Journal of Molecular Graphics and Modelling, 26(3), 652–655. https://doi.org/10.1016/j.jmgm.2007.03.011 doi:10.1016/j.jmgm.2007.03.011