Full Bibliography
1. Flory, P.J. and Jernigan, R.L. Second and fourth moments of chain molecules. J. Chem. Phys. 1965; 42: 3509-3519.
2. Leonard, W.J., Jr., Jernigan, R.L. and Flory, P.J. Dipole moments in relation to configuration of n-alkane chains bearing alpha, omega dipolar substituents. J. Chem. Phys. 1965; 43: 2256-2261.
3. Abe, A., Jernigan, R.L. and Flory, P.J. Conformational energies of n-alkanes and the random configuration of higher homologs including polymethylene. J. Amer. Chem. Soc. 1966; 88: 631-639.
4. Jernigan, R.L. and Flory, P.J. Optical anisotropy of chain molecules. Theory of depolarization of scattered light with application to n-alkanes. J. Chem. Phys. 1967; 47: 1999-2007.
5. Jernigan, R.L. and Flory, P.J. Configurational distributions for finite chain molecules. Polym. Prepr. 1967; 8: 152-153.
6. Jernigan, R.L. Configurational statistics of chain molecules with applications to normal alkanes. Thesis. Stanford University 1967, 198pp.
7. Jernigan, R.L. and Flory, P.J. Configurational distributions for finite chain molecules. J. Poly. Sci. Pt. C. 1968; 25: 69-72.
8. Flory, P.J. and Jernigan, R.L. Rayleigh scattering by real chain molecules. Polym. Prepr. 1968; 9: 267-272.
9. Flory, P.J. and Jernigan, R.L. Rayleigh scattering by real chain molecules. J. Amer. Chem. Soc. 1968; 90: 3128-3134.
10. Flory, P.J., Jernigan, R.L. and Tonelli, A.E. Strain birefringence of polymer chains. J. Chem. Phys. 1968; 48: 3822-3823.
11. Flory, P.J. and Jernigan, R.L. The Kerr effect in polymer chains. J. Chem. Phys. 1968; 48: 3823-3824.
12. Jernigan, R.L. and Flory, P.J., Configurational correlations in chain molecules. J. Chem. Phys. 1969; 50: 4165-4177.
13. Jernigan, R.L. and Flory, P.J. Moments of chain vectors for models of polymer chains. J. Chem. Phys. 1969; 50: 4178-4185.
14. Jernigan, R.L. and Flory, P.J. Distribution functions for chain molecules. J. Chem. Phys. 1969; 50: 4185-4200.
15. Jernigan, R.L. Internal relaxation in short chains bearing terminal polar groups. Polym. Prepr. 1971; 12: 121-127.
16. Jernigan, R.L. Internal relaxation in short chains bearing terminal polar groups. In: Karasz, F.E. (Ed.) Dielectric Properties of Polymers. New York: Plenum Press, 1972; 99-128.
17. Jernigan, R.L., Ferretti, J.A. and Weiss, G.H. Models of time dependent behavior of polypeptides in the helix-random coil transition region. Application to NMR spectra. Poly. Prepr. 1972; 10: 941-945.
18. Ferretti, J.A. and Jernigan, R.L. NMR spectra of poly - gamma -benzyl-L-glutamate in the helix coil transition region. Polym. Prepr. 1972; 10: 946-951.
19. Jernigan, R.L., Ferretti, J.A. and Weiss, G.H. Helix lifetimes within the conformational transition region. A random walk model. Macromolecules 1973; 6: 684-687.
20. Ferretti, J.A. and Jernigan, R.L. Conformational lifetimes in the helix-random coil transition region by nuclear magnetic resonance with application to poly (gamma-benzyl-L-glutamate). Macromolecules 1973; 6: 687-692.
21. Ferretti, J.A., Jernigan, R.L. and Weiss, G.H. Polypeptide helix lifetimes in the helix-random coil transition region. Application to NMR spectra. J. Polym. Sci. Pt. C. 1973; 42: 1051-1059.
22. Jernigan, R.L. and Weiss, G.H. An equivalent chain model of configurational distributions. Polym. Prepr. 1973; 14: 214-219.
23. Ferretti, J.A., Jernigan, R.L. and Miller, W.G. Missing magnitudes. Nature 1973; 245: 59-60.
24. Jernigan, R.L. and Ferretti, J.A. Mean configurational relaxation rates in finite length polypeptides. J. Chem. Phys. 1975; 62: 2519-2529.
25. Jernigan, R.L., and Thompson, D.S., Flexible polymers. In: O'Konski, C.T. (Ed.) Molecular Electro-optics. New York: Marcel Dekker, 1976; 159-205.
26. Jernigan, R.L. and Szu, S.C. Polypeptide relaxation rates with configurationally dependent internal friction. J. Polym. Sci. 1976; 54: 271-281.
27. Wu, T.T., Szu, S.C., Jernigan, R.L., Bilofsky, H. and Kabat, E.A. Prediction of beta-sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 x 20 table for evaluation of nearest-neighbors on conformations of middle amino acids in proteins. Biopolymers 1978; 17: 555-572.
28. Szu, C. and Jernigan, R.L. DNA conformational kinetics. Biopolymers 1979; 18: 83-100.
29. Bourgeois, S., Jernigan, R.L., Kabat, E.A., Szu, S.C. and Wu, T.T. Composite predictions of secondary structure of lac repressor. Biopolymers 1979; 18: 2625-2643.
30. Jernigan, R.L., and Szu, S.C. Conformational energy minimization in the approximation of limited range interactions. Macromolecules 1979; 12: 1156-1159.
31. Jernigan, R.L., Miyazawa, S. and Szu, S.C. Stabilization of regular conformational regions in proteins by intraregion electrostatic interactions. Macromolecules 1980; 13: 518-525.
32. Jernigan, R.L., Miyazawa, S. and Szu, S.C. Electrostatic interactions and secondary structures in proteins. Biophys. J. 1980; 32: 93-95.
33. Jernigan, R.L. and Miyazawa, S. Kerr effects of flexible macromolecules. In: Krause, S. (Ed.) Molecular Electro-Optics. New York: Plenum Press, 1981; 163-179.
34. Miyazawa, S. and Jernigan, R.L. Equilibrium folding and unfolding pathways for a model protein. Biopolymers 1982; 21: 1333-1363.
35. Miyazawa, S. and Jernigan, R.L. Most probable intermediates in protein folding-unfolding with a non-interacting globule-coil model. Biochemistry 1982; 21: 5203-5213.
36. Minuk, G.Y., Waggoner, J.G., Jernigan, R.L., Nicolle, L.E., Postl, B. and Hoofnagle, J.H. Prevalence of antibody to hepatitis A virus in a Canadian Inuit community. Can. Med. Assoc. J. 1982; 127: 850-852.
37. Jernigan, R.L. and Miyazawa, S. Equilibrium folding-unfolding pathways of model proteins: effect of myoglobin-heme contacts. Biopolymers 1983; 22: 79-85.
38. Miyazawa, S. and Jernigan, R.L. Equilibrium folding pathways for model proteins. J. Stat. Phys. 1983; 30: 549-559.
39. Church, W.R., Jernigan, R.L., Toole, J., Hewick, R.M., Knopf, J., Knutson, G.J., Nesheim, M.E., Mann, K.G. and Fass, D.N. Coagulation factors V and VIII and ceruloplasmin constitute a family of structurally related proteins. Proc. Natl. Acad. Sci. USA 1984; 81: 6934-6937.
40. Miyazawa, S. and Jernigan, R.L. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985; 18: 534-552.
41. Sarai, A., and Jernigan, R.L., A model of the strain-induced B-Z transition. J. Biomol. Struc. & Dyn. 1985; 2: 767-784.
42. Jernigan, R.L., Sarai, A., Ting, K.-L. and Nussinov, R. Hydrophobic interactions in the major groove can influence DNA local structure. J. Biomol. Str. Dyn. 1986; 4: 41-48.
43. Sarai, A., Jernigan, R.L., Shapiro, B. and Nussinov, R. Relationship between curved DNA conformations and slow gel migration. J. Biomol. Str. Dyn. 1987; 4: 561-567.
44. Margalit, H., Shapiro, B.A., Nussinov, R., Owens, J. and Jernigan, R.L. Helix stability in prokaryotic promoter regions. Biochemistry 1988; 27: 5179-5188.
45. Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R.L. Sequence dependence of DNA conformations: Means and fluctuations. In: Olson, W.K., Sarma, M.H., Sarma, R.H., and Sundaralingam, M. (Eds) Structure & Expression, Vol. 3: DNA Bending & Curvature, 1988; 213-223.
46. Nussinov, R., Sarai, A., Wang, D. and Jernigan, R.L. Sequence context of homooligomer tracts in eukaryotic genomes: Some DNA conformational implications. In: Olson, W.K., Sarma, M.H., Sarma, R.H., and Sundaralingam, M. (Eds.) Structure & Expression, Vol. 3: DNA Bending & Curvature, 1988; 129-138.
47. Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R.L. Origin of DNA helical structure and its sequence dependence. Biochemistry 1988; 27: 8498-8502.
48. Jernigan, R.L., Sarai, A., Covell, D.G. and Mazur, J. Exhaustive enumeration and evaluation of feasible conformations for double helix DNA and for folded proteins. International Conference on Supercomputers, Boston, 1988; 1: 197-200.
49. Nussinov, R., Sarai, A., Smythers, G.W. and Jernigan, R.L. Sequence context of oligomer tracts in eukaryotic DNA: Biological and conformational implications. J. Biomol Str. Dyn. 1988; 6: 543-562.
50. Ben-Naim, A., Ting, K.-L. and Jernigan, R.L. Solvation thermodynamics of biopolymers I. Separation of the volume and surface interactions with estimates of the volume and surface interactions. Biopolymers 1989; 28: 1309-1325.
51. Ben-Naim, A., Ting, K.-L. and Jernigan, R.L. Solvation thermodynamics of biopolymers II. Correlations between functional groups. Biopolymers 1989; 28: 1327-1337.
52. Mazur, J., Sarai, A. and Jernigan, R.L. Sequence dependence of the B-A conformational transition of DNA. Biopolymers 1989; 28: 1223-1233.
53. Nussinov, R., Sarai, A., Smythers, G.W., Wang, D. and Jernigan, R.L. Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA. Biochim. Biophys. Acta, 1989; 1008: 329-338.
54. Covell, D.G. and Jernigan, R.L. Lattice models of globular proteins. Correlations between sites. International Conference on Supercomputers, Santa Clara, 1989, Vol. II, 357-360, 1989.
55. Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R.L. Sequence dependence of DNA conformational flexibility. Biochemistry 1989; 28: 7842-7849.
56. Nussinov, R., Sarai, A., Smythers, G.W., Wang, D. and Jernigan, R.L. Strong patterns in homooligomer tract occurrences in non-coding and in potential regulatory sites in eukaryotic genomes. J. Biomol. Str. Dyn. 1989; 7: 707-722.
57. Jernigan, R., Davies, D. and Scheraga, H. Experimental and theoretical protein folding. J. Biomol. Str. Dyn. 1989; 6: 1039-1043.
58. Mazur, J., Sarai, A. and Jernigan, R.L. Interaction range in B-form DNA helices. Proc. 12th IMACS World Congress, International Association for Mathematics and Computers in Simulation, Paris, 1989; 8-12.
59. Ben-Naim, A., Ting, K.-L. and Jernigan, R.L., Solvent effect on binding thermodynamics of biopolymers. Biopolymers, 1990; 29: 901-919.
60. Sumner, S.C.J., Gallagher, K.S., Davis, D.G., Covell, D.G., Jernigan, R.L., and Ferretti, J.A., Conformational analysis of the tachykinins in solution: Substance P and physalaemin. J. Biomol. Str. Dyn. 1990; 8: 687-707.
61. Goodman, S., Yang, C.-C., Nash, H., Sarai, A. and Jernigan, R.L. Bending of DNA by IHF protein. In: Sarma, R.H. and Sarma, M.H. (Eds.) "Structure and Methods: DNA Protein Complexes and Proteins", Vol. 2, Adenine Press, NY, 1990; 51-62.
62. Raghunathan, G., Jernigan, R.L., Ting, K.-L. and Sarai, A., Solvation effects on the sequence variability of DNA double helical conformations. J. Biomol. Str. Dyn. 1990; 8: 187-198.
63. Jernigan, R.L. DNA conformational fluctuations. In: Lavery, R. (Ed.) Proceedings of Cecam Workshop on "Nucleic Acids and the Information They Convey: Modeling Sequence Effects on the Conformation, Flexibility and Interactions of DNA", 1990; 87-92.
64. Covell, D.G., and Jernigan, R.L. Conformations of folded proteins in restricted spaces. Biochemistry 1990; 29: 3287-3294.
65. Jernigan, R.L., Margalit, H. and Covell, D.G. Coarse graining conformations: a peptide binding example. In: Beveridge, D.L. and Lavery, R. (Eds.) "Theoretical Biochemistry and Molecular Biophysics Vol. 2: Proteins", 1991; 69-76.
66. Bohacek, R.S., Strauss, U.P. and Jernigan, R.L. Configurational statistics of methyl vinyl ether-maleic anhydride copolymer: selection of important atomic interactions and conformations. Macromolecules 1991; 24:731-739.
67. Jernigan, R.L. and Covell, D.G. Compact protein conformations. In: "Proteins: Structure, Dynamics and Design", ESCOM Science Publishers B.V.,Leiden, 1991; pp 346-351.
68. Raghunathan, G., Jernigan, R.L., Miles, H.T. and Sasisekharan, V. Conformational feasibility of a hairpin with two purines in the loop 5'-d(GGTACIAGTACC-3'. Biochemistry 1991; 30: 782-788.
69. Jacchieri, S. and Jernigan, R.L. Variable ranges of interactions in polypeptide conformations with a method to complement molecular modeling. Biopolymers 1992; 32: 1327-1388.
70. Zhurkin, V. B., Ulyanov, N. B., Gorin, A. A. and Jernigan, R. L. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc. Natl. Acad. Sci. USA 1991; 88: 7046-7050.
71. Mazur, J. and Jernigan, R.L. The distance-dependent dielectric constants and their application to double-helix DNA. Biopolymers 1991; 31: 1615-1629.
72. Jernigan, R.L. Generating general shapes and conformations with regular lattices, for compact proteins. In: Sarma, R.H. & Sarma, M.H. (Eds.) "Structure and Function: Proceedings of Seventh Conversation in Biomolecular Stereodynamics", Vol. 2, Adenine Press, 1991; 169-182.
73. Sumner, S. C. J., Jiang, S.-P., Jernigan, R. L. and Ferretti, J.A. Conformational analysis of receptor selective tachykinin analogs: senktide and septide. J. Biomol. Str. Dyn. 1992; 10: 429-439.
74. Jernigan, R.L. Protein folds. Curr. Opin. Str. Biol. 1992; 2: 248-256.
75. Olson, W.K., Marky, N.L., Jernigan, R.L. and Zhurkin, V.B. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 1993; 232: 530-554.
76. Miyazawa, S. and Jernigan, R.L. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Prot. Eng. 1993; 6: 267-278.
77. Jernigan, R.L. and Ting, K.-L. A new approach to protein folding calculations. In: Doniach, S. (Ed.) "Statistical Mechanics, Protein Structure and Protein Substrate Interactions", Plenum Press, NY, 1994; 317-326.
78. Lustig, B., Covell, D. and Jernigan, R.L. Conformations of t-RNA: Base Pairing and Stacking. J. Biol. Str. Dyn., 1994; 12: 145-161.
79. Young, L., Covell, D. and Jernigan, R.L. A Role for surface hydrophobicity in protein-protein recognition. Prot. Sci. 1994; 3: 717-729.
80. Bahar, I. and Jernigan, R.L. Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions.
Biophys. J. 1994; 66: 454-466.
81. Bahar, I. and Jernigan, R.L. Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. Biophys. J. 1994; 66:467-481.
82. Miyazawa, S. and Jernigan, R.L. Protein stability changes for single substitution mutants and the extent of local compactness in the denatured state. Prot. Eng., 1994; 7:1209-1220.
83. Zhurkin, V.B., Raghunathan, G., Ulyanov, N.B., Camerini-Otero, R.D. and Jernigan, R.L. A parallel DNA triplex as a model for the intermediate in homologous recombination. J. Mol. Biol., 1994; 239:181-200.
84. Jiang, S.-P., Jernigan, R.L., Ting, K.-L., Syi, J.-L. and Raghunathan, G. Stability and Cooperativity of Nucleic Acid Base Triplets. J. Biomol. Str. Dyn. 1994; 4: 383-399.
85. Zhurkin, V. B., Raghunathan, G., Ulyanov, N.B., Camerini-Otero, R.D. and Jernigan, R.L. Recombination triple helix, R-form DNA. A stereochemical model for recognition and strand exchange. in "Structural Biology: State of the Art", Eds. R.H. Sarma and M.H. Sarma, Adenine Press, 1994; 43-66.
86. Kim, M. G., Zhurkin, V.B., Jernigan, R. L. and Camerini-Otero, R.D. Parallel DNA triplexes and homolgous recombination. in "Structural Biology: State of the Art", Eds. R.H. Sarma and M.H. Sarma, Adenine Press, 1994; Vol. II: 67-74.
87. Jernigan, R., Raghunathan, G. and Bahar, I. Characterization of interactions and metal ion binding sites in proteins. Curr. Opin. Str. Biol. 1994; 4: 256-263.
88. Jiang, S.-P., Raghunathan, G., Ting, K.-L., Xuan, J.C. and Jernigan, R.L. Geometries, Charges, Dipole Moments and Interaction Energies of Normal, Tautomeric and Novel Bases. J. Biomol. Str. Dyn. 1994; 12: 367-382
89. Kim, M.G., Zhurkin, V.B., Jernigan, R.L. and Camerini-Otero, R.D. Probing the structure of a putative intermediate in homologous recombination: The third strand in the parallel DNA triplex is in contact with the major groove of the duplex. J. Mol. Biol., 1995; 247: 874-889.
90. Mazur, J. and Jernigan, R.L. Comparison of Rotation Models for Describing DNA Conformations: Application to Static and Polymorphic Forms. Biophys. J., 1995; 68: 1472-1489.
91. Jernigan, R.L., Young, L., Covell D.G. and Miyazawa, S. Applications of empirical amino acid potential functions. in “Modelling of Biomolecular Structures and Mechanisms.” A. Pullman, et al. (Eds.), Kluwer Acad. Publ. 1995; 151-166.
92. Lustig, B., Lin, N.H., Smith, S.M., Jernigan, R.L. and Jeang, K.-T. A Small Modified Hammerhead Ribozyme and Its Conformational Characteristics Determined by Mutagenesis and Lattice Calculation. Nucl. Acids Res. 1995; 23: 3531-3538.
93. Wallqvist, A., Jernigan, R.L. and Covell, D.G. A Preference-Based Free-Energy Parameterization of Enzyme-Inhibitor Binding. Applications to HIV-1-Protease Inhibitor Design. Prot. Sci. 1995; 4: 1881-1903.
94. Lustig, B. and Jernigan, R.L. Consistencies of Individual DNA Base-Amino Acid Interactions in Structures and Sequences. Nucl. Acids Res. 1995; 23: 4707-4711.
95. Miyazawa, S. and Jernigan, R.L. Residue-Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term for Simulation and Threading. J. Mol. Biol. 1996; 256: 623-644.
96. Mazur, J., Jernigan, R.L., and Sarai, A. Constructing Optimal Backbone Segments for Joining Fixed DNA Base Pairs. Biophys. J. 1996; 71: 1493-1506.
97. Sarai, A., Jernigan, R.L. and Mazur, J. Interdependence of Conformational Variables in Double Helical DNA. Biophys. J. 1996; 71: 1507-1518.
98. Bahar, I. and Jernigan, R.L. Coordination geometry of non-bonded residues in globular proteins, Folding & Design 19961: 357-370.
99. Jernigan, R.L. and Bahar, I. Structure-derived Potentials and Protein Simulations. Curr. Opin. Struct. Biol. 1996; 6: 195-209.
100. Naor, D., Fischer, D., Jernigan, R.L., Wolfson, H. J. and Nussinov, R. Amino Acid Pair Interchanges at Spatially Conserved Locations. J. Mol. Biol. 1996;256: 924-938.
101. Teplukhin, A.V., Zhurkin, V.B., Jernigan, R. and Poltev, V.I. Monte Carlo Modeling of DNA Hydration. Poly(A)-Water Interaction in the Major Groove Stabilizes the B’ Conformation. Molec. Biol. 1996; 30: 75-84.
102. Bahar, I., Atilgan, A.R., Jernigan, R.L. and Erman, B. Understanding the
recognition of protein structural classes by amino acid composition. Proteins, 1997; 29: 172-185.
103. Bahar, I. and Jernigan, R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 1997; 266: 195-214.
104. Bahar, I. and Jernigan, R.L. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins, 1997; 29: 292-308.
105. Lustig, B., Arora, S. and Jernigan, R.L., RNA base-amino acid interaction strengths derived from structures and sequences. Nucl. Acids Res., 1997; 25: 2562-2565.
106. Erman, B., Bahar, I. and R. L. Jernigan, R.L. Equilibrium states of rigid bodies with multiple interaction sites. Application to protein helices. J. Chem. Phys., 1997; 107: 2046-2059.
107. Kloczkowski, A. and Jernigan, R.L. Efficient Method to Count and Generate Compact Protein Lattice Conformations. Macromolecules, 1997; 30: 6691-6694.
108. Bahar, I., Erman, B, Haliloglu, T. and Jernigan, R.L. Efficient characterization of collective motions and inter-residue correlations in proteins by low resolution simulations. Biochemistry, 1997; 36: 13512-13523.
109. Raghunathan, G. and Jernigan, R.L., Ideal architecture of residue packing and its observation in protein structures. Protein Sci. 1997; 6: 2072-2083, 2485.
110. Kloczkowski, A. and Jernigan, R.L. Computer generation and enumeration of compact self-avoiding walks within simple geometries on lattices. Comput. Theoret. Polym. Sci. 1997; 7: 163-173.
111. Covell, D.G., Jernigan, R.L. and Wallqvist, A. Taking Aim at HIV-1 Protease: Mutable Inhibitor Targets within Common Binding Pockets. J. Mol. Struct. (Theoret. Biochem.) 1998; 423: 93-100.
112. Bahar, I., Wallqvist, A., Covell, D.G. and Jernigan, R.L. Correlation between Native State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model. Biochemistry , 1998; 37: 1067-1075.
113. Jernigan, R.L. and Bahar, I. Conformational search: Proteins. In ”The Encyclopedia of Computational Chemistry,” Schleyer, P. V.R.; Allinger, N. L., Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R. (Eds.); John Wiley & Sons: Chichester, 1998; 562-570.
114. Durell, S.R., Jernigan, R.L., Appella, E., Nagaich, A.K., Harrington, R.E. and Zhurkin, V.B. DNA Bending Induced by Tetrameric Binding of the p53 Tumor Suppressor Protein: Steric Constraints on Conformation. In: Structure, Motion, Interaction and Expression of Biological Macromolecules. Proceedings of the Tenth Conversation, 1997. Sarma, R.H and Sarma, M.H. (Eds.) New York: Adenine Press, 1998, Vol. 2, pp. 277-296.
115. Mandel-Gutfreund, Y., Margalit, H., Jernigan, R.L. and Zhurkin, V.B. A role for CH...O interactions in protein-DNA recognition. J. Mol. Biol. 1998; 277: 1129-1140.
116. Demirel, M.C., Atilgan, A.R., Jernigan, R.L., Erman, B. and Bahar, I. Identification of kinetically hot residues in proteins. Protein Sci. 1998; 7: 2522-2532.
117. Kloczkowski, A. and Jernigan, R.L. Transfer matrix method for enumeration and generation of compact self-avoiding walks. I. Square lattices. J. Chem. Phys. 1998; 109: 5134-5146.
118. Kloczkowski, A. and Jernigan, R.L. Transfer matrix method for enumeration and generation of compact self-avoiding walks. II. Cubic lattice. J. Chem. Phys. 1998; 109: 5147-5159.
119. Bahar, I. and Jernigan, R.L. Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms. J. Mol. Biol. 1998; 281: 871-884.
120. Keskin, O, Bahar, I., Badretdinov, A.Y., Ptitsyn, O.B. and Jernigan, R.L. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Prot. Sci 1998; 7: 2578-2586.
121. Lustig, B., Bahar, I. and Jernigan, R.L. RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 AND BIV TAR RNA because of improved conformational access. Nucl. Acids Res., 1998; 26: 5212-5217.
122. Miyazawa, S. and Jernigan, R.L. Self-consistent estimation of inter-residue contact energies based on a residue mixture approximation for proteins. Proteins , 1999; 34: 39-68.
123. Bahar, I., Erman, B., Jernigan, R.L. and Covell, D.G. Collective motions in HIV-1 Reverse Transcriptase: Examination of flexibility and enzyme function. J. Mol. Biol. 1999; 285: 1023-1037.
124. Nagaich, A.K., Zhurkin, V.B., Durell, S.R., Jernigan, R.L., Appella, E. and Harrington, R.E. p53-Induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting. Proc. Natl. Acad. Sci. USA 1999; 96: 1875-1880.
125. Miyazawa, S. and Jernigan, R.L. Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition. Proteins 1999; 36: 347-356.
126. Miyazawa, S. and Jernigan, R.L. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999; 36: 357-369.
127. Bahar, I. and Jernigan, R.L. Cooperative Fluctuations and Subunit Communication in Tryptophan Synthase. Biochemistry 1999; 38: 3478-3490.
128. Jernigan, R.L., Demirel M.C. and Bahar, I. Relating Structure to Function through the Dominant Modes of Motion of DNA Topoisomerase II Int. J. Quant. Chem. (B. Pullman Memorial Volume) 1999; 75: 301-312.
129. Bahar, I. and Jernigan, R.L. Geometric Regularities among Bonded and Non-bonded Residues in Proteins. In “Perspectives in Structural Biology” (GN Ramachandran Volume) M. Vijayan, N. Yathindra and A.S. Kolaskar Eds., Indian Academy of Sciences, Universities Press, Hyderabad, 1999; 209-225.
130. Kloczkowski, A. and Jernigan, R.L. Contacts Between Segments in the Random Flight Model of Polymer Chains. Comp. Theoret. Polym. Sci. (special Suter Issue) 1999; 9: 285-294.
131. Keskin, O., Jernigan, R.L. and Bahar, I. Proteins with Similar Architecture Exhibit Similar Large-scale Dynamic Behavior. Biophys. J. 2000; 78: 2093-2106.
132. Keskin, O., Bahar, I., Jernigan, R. L., Beutler, J.A., Shoemaker, R. H., Sausville, E. A. and Covell, D.G. Characterization of Anticancer Agents by Their Growth Inhibitory Activity and Relationships to Mechanism of Action and Structure. Anti-Cancer Drug Design 2000; 15: 79-98.
133. Miyazawa, S. and Jernigan, R.L. Identifying sequence-structure pairs undetected by sequence alignments. Prot. Eng. 2000;13: 459-475.
134. Jernigan, R.L., Bahar, I., Covell, D. G., Atilgan, A. R., Erman, B. and Flatow, D. T. Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step. J. Biomol. Struct. Dyn. 2000, Vol.: Conversation 11, Issue 1, pp 49-55.
135. Harrington, R.E., Zhurkin, V.B., Durell, S.R., Jernigan, R.L., Nagaich, A.K. and Appella, E., A. Structural model for the p53 Complex with DNA Response Elements: Implications for p53 Function and Future Research Directions. In “Proteome and Protein Analysis”, Eds. R.M. Kamp, D. Kyriakidis, and Th. Choli-Papadopoulou, Springer-Verlag, Berlin, pp 257-272.
136. Atilgan, A.R., Durell, S. R., Jernigan, R. L., Demirel, M.C., Keskin, O., and Bahar, I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 2001; 80: 505-515.
137. Kloczkowski, A., Ting, K.-L., Jernigan, R.L. and Garnier, J. Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information. Polymer 2001; 43: 441-449.
138. Tolstorukov M.Y., Ivanov V.I., Malenkov G.G., Jernigan R.L., Zhurkin V.B. Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J. 2001; 81: 3409-21.
139. Doruker P., Jernigan R.L., and Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 2002; 23: 119-27.
140. Mansfield M.L., Covell D.G., and Jernigan R.L. A new class of molecular shape descriptors. 1. Theory and properties. J. Chem. Inf. Comput. Sci. 2002; 42: 259-73.
141. Keskin O., Bahar I., Flatow D., Covell D.G., Jernigan R.L. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 2002; 41: 491-501.
142. Ting K.L., and Jernigan R.L. Identifying a Folding Nucleus for the Lysozyme/alpha-Lactalbumin Family from Sequence Conservation Clusters. J. Mol. Evol. 2002; 54: 425-36.
143. Keskin O., Durell S.R., Bahar I., Jernigan R.L., and Covell D.G. Relating molecular flexibility to function: a case study of tubulin. Biophys. J. 2002; 83:663-680.
144. Bagci, Z., Jernigan, R.L. and Bahar, I. Residue packing in proteins: Uniform distribution on a coarse-grained scale. J. Chem. Phys. 2002; 116, 2269-2276.
145. Kim, M.K., Jernigan, R..L. and Chirikjian, G.S. Efficient generation of feasible
pathways for protein conformational transitions. Biophys. J. 2002; 83: 1620-1630.
146. Kim, M.K., Jernigan, R.L.and Chirikjian, G.S. Elastic models of conformational transitions in macromolecules. J. Mol. Graph. Model 2002; 21: 151-160.
147. Doruker, P., Jernigan, R.L., Navizet, I. And Hernandez, R. Important fluctuation dynamics of large protein structures are preserved upon renormalization. Int. J. Quantum Chem. 2002; 90: 822-837.
148. Kloczkowski, A., Ting, K.-L., Jernigan, R.L. and Garnier, J. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins
2002; 49: 154-166.
149. Kloczkowski, A. and Jernigan, R.L. Loop folds in proteins and evolutionary conservation of folding nuclei. J. Biomol. Struct. Dyn. 2002; 20: 323-325.
150. Keskin, O., Durell, S.R., Bahar, I., Jernigan, R.L. and Covell, D.G. Relating molecular flexibility to function: A case study of tubulin. Biophys. J. 2002; 83: 663-680.
151. Bagci, Z., Jernigan, R.L. and Bahar, I. Residue coordination in proteins conforms to the closest packing of spheres. Polymer 2002; 43: 451-459.
152. Mazur, J., Jernigan, R.L. and Sarai A. Conformational Effects of Stretching DNA. Molecular Biology (transl. from Russian) 2003; 37: 240-249.
153. Bagci, Z., Kloczkowski, A., Jernigan, R.L. and Bahar, I. The origin and extent of coarse-grained regularities in protein internal packing. Proteins -Struct Funct. Genet. 2003; 53: 56-67.
154. Kim, M.K., Jernigan, R.L. and Chirikjian, G.S. An elastic network model of HK97 capsid maturation.
J. Struct. Biol. 2003; 143: 107-117.
155. Miyazawa, S. and Jernigan, R.L. Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space. Proteins -Struct. Funct. Genet. 2003; 50: 35-43.
156. Doruker, P. and Jernigan, R.L. Functional motions can be extracted from on-lattice construction of protein structures. Proteins 2003; 53:174-181.
157. Navizet, I., Lavery, R. and Jernigan, R.L. Myosin flexibility: Structural domains and collective vibrations. Proteins, 2004; 54: 384-393.
158. Kloczkowski, A., Sen, T.Z. and Jernigan, R.L. The Transfer Matrix Method for Lattice Proteins – An Application with Cooperative Interactions. Polymer 2004; 45: 707-716.
159. Kurkcuoglu, O., Jernigan, R.L. and Doruker, P. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions. Polymer, 2004; 45: 649-657.
160. Kloczkowski, A. and Jernigan, R.L. Introduction to “Protein Conformational Computations” - a special issue of Polymer, 2004; 45: 507.
161. Shchyolkina, A.K., Kaluzhny, D.N., Borisova, O.F., Hawkins, M.E., Jernigan, R.L., Jovin, T.M., Arndt-Jovin, D.J. a nd Zhurkin, V.B. Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin. Nucl. Acids Res., 2004; 32: 432-440.
162. Tolstorukov, M.Y., Jernigan, R.L. and Zhurkin, V.B. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J. Mol. Biol. 2004; 337: 65-76.
163. Wang, Y., Rader, A.J., Bahar, I. and Jernigan, R.L. Global Ribosome Motions Revealed with Elastic Network Model. J. Struct. Biol., 2004; 147: 302-314.
164. Kundu, S. and Jernigan, R.L. Molecular Mechanism of Domain Swapping in Proteins:
An Analysis of Slower Motions. Biophys. J. 2004; 86:3846-3854.
165. Sen, T.Z., Kloczkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K.M., Wang, C.Z., Ihm, Y., Cao, H., Gu, X. and Dobbs, D. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods, BMC Bioinformatics 2004; 5: 205.
166. Kloczkowski, A., Sen, T.Z and Jernigan, R.L. Promiscuous vs. native protein function. Insights from studying collective motions in proteins by elastic network models, J. Biomol. Struct. Dyn., 2005; 22: 621-624, 2005.
167. Kim, M.K., Jernigan, R.L. and Chirikjian, G.S. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies, Biophys. J. 2005; 89:43-55.
168. Pokarowski, P., Kloczkowski, A., Jernigan, R.L., Kothari, N.S., Pokarowska, M. and Kolinski, A. Inferring ideal amino acid interaction forms from statistical protein contact potentials, Proteins: Struct. Funct. Bioinf. 2005; 59: 49-57.
169. Liao, H., Yeh, W., Chiang, D., Jernigan, R.L. and Lustig, B. Protein sequence entropy is closely related to packing density and hydrophobicity. Prot. Eng. Des. Select. 2005; 18: 59-64.
170. Miyazawa, S. and Jernigan, R.L. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? J. Chem. Phys. 2005; 122: 024901.
171. Yan, A. and Jernigan R.L. How do sidechains orient globally in protein structures? Proteins 2005; 61:513-522.
172. Cheng, H., Sen, T.Z., Kloczkowski, A., Margaritis, D. and Jernigan, R.L. Prediction of protein secondary structure by mining structural fragment database, Polymer 2005; 46:4314-4321.
173. Sen, T.Z., Jernigan, R.L., Garnier J., and Kloczkowski, A. GOR V server for protein Secondary structure prediction, Bioinformatics, 2005; 21:2787-2788.
174. Wang, Y. and Jernigan, R.L. Comparison of tRNA Motions in the Free and Ribosomal Bound Structures Biophys. J., 2005; 89:3399-3409.
175. Cui, F., Jernigan, R., and Zu, Z. (2005) Refinement of NMR-determined protein structures with database derived distance constraints. J. Bioinformatics and Comp. Biol., 2005;3:1315-1329.
176. Kurkcuoglu, O., Jernigan, R.L. and Doruker, P. Collective dynamics of large proteins from mixed coarse-grained elastic network model. QSAR Comb. Sci., 2005; 24:443-448.
177. Sen, T.Z. and Jernigan, R.L. Optimizing cutoff distances and spring constants for the Gaussian Network Model of ATP-binding proteins, in “Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems,” 2006, Eds. I. Bahar and Q. Cui, Chapman and Hall/CRC, Boca Raton, pp 171-186.
178. Kurkcuoglu, O., Jernigan, R.L. and Doruker, P. Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks, Biochemistry, 2006;45:1173-1182.
179. Song G., and Jernigan R.L. An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins, 2006;63:197-209.
180. Terribilini, M., Lee, J-H., Yan, C., Jernigan, RL. Honavar, V. and Dobbs, D. (2006). Identifying
Interactions in ”Recalcitrant” Proteins. Predicted Protein and RNA binding sites in REV proteins of
HIV and EIAV agree with experimental data. In: Proceedings of the Pacific Symposium on
Biocomputing (PSB 06). Singapore: World Scientific Press. pp. 415-426.
181. Terribilini, M., Lee, J.H., Yan, C., Jernigan, R.L., Honavar, V., and Dobbs, D. (2006). Prediction of Protein-RNA Interfaces. RNA, 2006; 12: 1450-1462.
182. Sen, T.Z., Feng, Y., Garcia, J.V., Kloczkowski, A. and Jernigan, R.L. The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J. Chem. Thy. Comput., 2006; 2, 696-704.
183. Sen TZ, Kloczkowski A, Jernigan RL. A DNA-Centric Look at Protein-DNA Complexes. Structure, 2006; 14:1341-2.
184. Jernigan RL, Kloczkowski A. Packing regularities in biological structures relate to their dynamics. Methods Mol Biol, 2006; 350:251-76.
185. Sen TZ, Kloczkowski A, Jernigan RL. Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics. 2006; 7:355.
186. Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006;7:262.
187. Sen TZ, Cheng H, Kloczkowski A, Jernigan RL. A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining. Protein Sci., 2006; Sep 25; [Epub ahead of print]