In plain words: Proteins are involved in almost every important biological process at the molecular level. While such processes occur over time, a reasonably good description of them is often available using structural or static information. Our group is concerned with the exceptions to this rule. That is, when does the motion matter, and if so, how can we then describe these systems using theoretical and computational tools. But if the static information is sufficient, then we are also happy to develop tools that take advantage of this simpler case.

Protein Motion, Folding, Bioinformatics, and Binding

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Detailed summary in construction

Relevant references are:

• C. R. Locker and R. Hernandez; "A minimalist model protein with multiple folding funnels," Proc. Natl. Acad. Sci. USA 98, 9074-9079 (2001). (doi:10.1073/pnas.161438898)
• C. R. Locker and R. Hernandez, "Folding behavior of model proteins with weak energetic frustration," J. Chem. Phys. 120, 11292-11303 (2004). (doi:10.1063/1.1751394)
• C.-S. Liu, R. Hernandez, and G. B. Schuster; "The mechanism for radical cation transport in duplex DNA oligonucleotides," J. Am. Chem. Soc. 126, 2877-2884 (2004). (doi:10.1021/ja0378254)
• P. Doruker, R. L. Jernigan, I. Navizet and R. Hernandez; "The important fluctuation dynamics of large protein structures are preserved upon renormalization," Int. J. Quant. Chem. 90, 822-837 (2002). (In the Per-Olov Lowdin Festschrift issue.) (doi:10.1002/qua.955)
• S. Zhong, J. M. Moix, S. Quirk, and R. Hernandez; "Dihedral-angle information entropy as a gauge of secondary structure propensity," Biophys. J. (2006), in press.