Professor
Director, Baker Center
for Bioinformatics and Biological Statistics
Theoretical studies on the structures of proteins, nucleic acids, and
small molecules
Applications of theoretical studies to develop molecular models and
to select new drugs
Selected Publications
Wang, Y., Rader, A.J., Bahar, I. and Jernigan, R.L. (2004) Global ribosome
motions revealed with elastic network model. J. Struct. Biol.
147, 302-314.
Kundu, S. and Jernigan, R.L. (2004) Molecular mechanism of domain swapping
in proteins: an analysis of slower motions. Biophys. J. 86,
3846-3854.
Tolstorukov, M.Y., Jernigan, R.L. and Zhurkin, V.B. (2004) Protein-DNA
hydrophobic recognition in the minor groove is facilitated by sugar
switching. J. Mol. Biol. 337, 65-76.
Navizet, I., Lavery, R. and Jernigan, R.L. (2004) Myosin flexibility:
structural domains and collective vibrations. Proteins 54,
384-393.
Shchyolkina, A.K., Kaluzhny, D.N., Borisova, O.F., Hawkins, M.E., Jernigan,
R.L., Jovin, T.M., Arndt-Jovin, D.J. and Zhurkin, V.B. (2004) Formation
of an intramolecular triple-stranded DNA structure monitored by fluorescence
of 2-aminopurine or 6-methylisoxanthopterin. Nucleic Acids Res.
32, 432-440.
Miyazawa, S. and Jernigan, R.L. (2003) Long- and short-range interactions
in native protein structures are consistent/minimally frustrated in
sequence space. Proteins 50, 35-43.
Kim, M.K., Jernigan, R.L. and Chirikjian, G.S. (2003) An elastic network
model of HK97 capsid maturation. J. Struct. Biol. 143, 107-117.
Doruker, P. and Jernigan, R.L. (2003) Functional motions can be extracted
from on-lattice construction of protein structures. Proteins
53, 174-181.
Baran, R.H., Ko, H. and Jernigan, R.W. (2003) Methods for comparing
sources of strand compositional asymmetry in microbial chromosomes.
DNA Res. 10, 85-95.
Bagci, Z., Kloczkowski, A., Jernigan, R.L. and Bahar, I. (2003) The
origin and extent of coarse-grained regularities in protein internal
packing. Proteins 53, 56-67.
Ting, K.L. and Jernigan, R.L. (2002) Identifying a folding nucleus for
the lysozyme/alpha-lactalbumin family from sequence conservation clusters.
J. Mol. Evol. 54, 425-436.
Kloczkowski, A., Ting, K.L., Jernigan, R.L. and Garnier, J. (2002) Combining
the GOR V algorithm with evolutionary information for protein secondary
structure prediction from amino acid sequence. Proteins 49,
154-166.
Kim, M.K., Jernigan, R.L. and Chirikjian, G.S. (2002) Efficient generation
of feasible pathways for protein conformational transitions. Biophys.
J. 83, 1620-1630.
Keskin, O., Bahar, I., Flatow, D., Covell, D.G. and Jernigan, R.L. (2002)
Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry
41, 491-501.
Keskin, O., Durell, S.R., Bahar, I., Jernigan, R.L. and Covell, D.G.
(2002) Relating molecular flexibility to function: a case study of tubulin.
Biophys. J. 83, 663-680.
Doruker, P., Jernigan, R.L. and Bahar, I. (2002) Dynamics of large proteins
through hierarchical levels of coarse-grained structures. J Comput.
Chem. 23, 119-127.
Tolstorukov, M.Y., Ivanov, V.I., Malenkov, G.G., Jernigan, R.L. and
Zhurkin, V.B. (2001) Sequence-dependent B<-->A transition in DNA
evaluated with dimeric and trimeric scales. Biophys. J. 81,
3409-3421.
Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin,
O. and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins
with an elastic network model. Biophys. J. 80, 505-515.
Miyazawa, S. and Jernigan, R.L. (2000) Identifying sequence-structure
pairs undetected by sequence alignments. Protein Eng. 13, 459-475.
Keskin, O., Jernigan, R.L. and Bahar, I. (2000) Proteins with similar
architecture exhibit similar large-scale dynamic behavior. Biophys.
J. 78, 2093-2106.
