Robert L. Jernigan
Publications
Note: copies of many of these papers are available at https://works.bepress.com/robert-jernigan/
1. Flory PJ, Jernigan RL. Second and fourth moments of chain molecules. J Chem Phys 1965;42:3509-3519.
2. Leonard WJ Jr., Jernigan RL, Flory PJ. 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 RL, Flory PJ. Conformational energies of n-alkanes and the random configuration of higher homologs including polymethylene. J Amer Chem Soc 1966;88:631-639.
4. Jernigan RL, Flory PJ. 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 RL, Flory PJ. Configurational distributions for finite chain molecules. Polym Prepr 1967;8: 152-153.
6. Jernigan RL. Configurational statistics of chain molecules with applications to normal alkanes. Thesis. Stanford University 1967, 198pp.
7. Jernigan RL, Flory PJ. Configurational distributions for finite chain molecules. J Polym Sci Pt. C. 1968; 25:69-72.
8. Flory PJ, Jernigan RL. Rayleigh scattering by real chain molecules. Polym Prepr 1968;9:267-272.
9. Flory PJ, Jernigan RL. Rayleigh scattering by real chain molecules. J. Amer. Chem. Soc. 1968;90: 3128-3134.
10. Flory PJ, Jernigan RL, Tonelli AE. Strain birefringence of polymer chains. J Chem Phys 1968;48:3822-3823.
11. Flory PJ, Jernigan RL. The Kerr effect in polymer chains. J Chem Phys 1968;48:3823-3824.
12. Jernigan RL, Flory PJ. Configurational correlations in chain molecules. J Chem Phys 1969;50:4165-4177.
13. Jernigan RL, Flory PJ. Moments of chain vectors for models of polymer chains. J Chem Phys 1969;50:4178-4185.
14. Jernigan RL, Flory PJ. Distribution functions for chain molecules. J Chem Phys 1969;50:4185-4200.
15. Jernigan RL. Internal relaxation in short chains bearing terminal polar groups. Polym Prepr 1971;12:121-127.
16. Jernigan RL. Internal relaxation in short chains bearing terminal polar groups. In: FE Karasz (Ed.) Dielectric Properties of Polymers. New York: Plenum Press, 1972;99-128.
17. Jernigan RL, Ferretti JA, Weiss GH. Models of time dependent behavior of polypeptides in the helix-random coil transition region. Application to NMR spectra. Polym Prepr 1972;10:941-945.
18. Ferretti JA, Jernigan RL. NMR spectra of poly - gamma -benzyl-L-glutamate in the helix coil transition region. Polym Prepr 1972;10:946-951.
19. Jernigan RL, Ferretti JA. Weiss GH. Helix lifetimes within the conformational transition region. A random walk model. Macromolecules 1973;6:684-687.
20. Ferretti JA, Jernigan RL. 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 JA, Jernigan RL, Weiss GH. 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 RL, Weiss GH. An equivalent chain model of configurational distributions. Polym Prepr 1973;14:214-219.
23. Ferretti JA, Jernigan RL, Miller WG. Missing magnitudes. Nature 1973;245:59-60.
24. Jernigan RL, Ferretti JA. Mean configurational relaxation rates in finite length polypeptides. J Chem Phys 1975;62:2519-2529.
25. Jernigan, RL, Thompson, DS. Flexible polymers. In: CT O'Konski (Ed.) Molecular Electro-optics. New York: Marcel Dekker, 1976;159-205.
26. Jernigan RL, Szu SC. Polypeptide relaxation rates with configurationally dependent internal friction. J Polym Sci 1976;54:271-281.
27. Wu TT, Szu SC, Jernigan RL, Bilofsky H, Kabat EA. 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, Jernigan RL. DNA conformational kinetics. Biopolymers 1979;18:83-100.
29. Bourgeois S, Jernigan RL, Szu SC, Kabat EA, Wu TT. Composite predictions of secondary structure of lac repressor. Biopolymers 1979;18:2625-2643.
30. Jernigan, RL, Szu, SC. Conformational energy minimization in the approximation of limited range interactions. Macromolecules 1979;12:1156-1159.
31. Jernigan RL, Miyazawa S, Szu SC. Stabilization of regular conformational regions in proteins by intraregion electrostatic interactions. Macromolecules 1980;13:518-525.
32. Jernigan RL, Miyazawa S, Szu SC. Electrostatic interactions and secondary structures in proteins. Biophys J 1980;32:93-95.
33. Jernigan, RL, Miyazawa S. Kerr effects of flexible macromolecules. In: S Krause (Ed.) Molecular Electro-Optics. New York: Plenum Press, 1981;163-179.
34. Miyazawa S, Jernigan RL. Equilibrium folding and unfolding pathways for a model protein. Biopolymers 1982;21:1333-1363.
35. Miyazawa S, Jernigan RL. Most probable intermediates in protein folding-unfolding with a non-interacting globule-coil model. Biochemistry 1982;21:5203-5213.
36. Minuk GY, Waggoner JG, Jernigan RL, Nicolle LE, Postl B, Hoofnagle, JH. Prevalence of antibody to hepatitis A virus in a Canadian Inuit community. Can Med Assoc J 1982;127:850-852.
37. Jernigan RL, Miyazawa S. Equilibrium folding-unfolding pathways of model proteins: effect of myoglobin-heme contacts. Biopolymers 1983;22:79-85.
38. Miyazawa S, Jernigan RL. Equilibrium folding pathways for model proteins. J Stat Phys 1983;30:549-559.
39. Church WR, Jernigan RL, Toole J, Hewick RM, Knopf J, Knutson GJ, Nesheim ME, Mann KG, Fass DN. 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, Jernigan RL. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
41. Sarai A, Jernigan RL. A model of the strain-induced B-Z transition. J Biomol Struc Dyn 1985;2:767-784.
42. Jernigan RL, Sarai A, Ting KL, Nussinov R. Hydrophobic interactions in the major groove can influence DNA local structure. J Biomol Struct Dyn 1986;4:41-48.
43. Sarai A, Jernigan RL, Shapiro B, Nussinov R. Relationship between curved DNA conformations and slow gel migration. J Biomol Struct Dyn 1987;4:561-567.
44. Margalit H, Shapiro BA, Nussinov R, Owens J, Jernigan RL. Helix stability in prokaryotic promoter regions. Biochemistry 1988;27:5179-5188.
45. Sarai A, Mazur J, Nussinov R, Jernigan RL. Sequence dependence of DNA conformations: Means and fluctuations. In: WK Olson, MH Sarma, RH Sarma, and M Sundaralingam (Eds) Structure & Expression, Vol. 3: DNA Bending & Curvature, 1988;213-223.
46. Nussinov R, Sarai A, Wang D, Jernigan RL. Sequence context of homooligomer tracts in eukaryotic genomes: Some DNA conformational implications. In: WK Olson, MH Sarma, RH Sarma, and M Sundaralingam (Eds.) Structure & Expression, Vol. 3: DNA Bending & Curvature, 1988;129-138.
47. Sarai A, Mazur J, Nussinov R, Jernigan RL. Origin of DNA helical structure and its sequence dependence. Biochemistry 1988; 27: 8498-8502.
48. Jernigan RL, Sarai A, Covell DG, 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 GW, Jernigan RL. Sequence context of oligomer tracts in eukaryotic DNA: Biological and conformational implications. J Biomol Struct Dyn 1988;6:543-562.
50. Ben-Naim A, Ting KL, Jernigan RL. 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 KL, Jernigan RL. Solvation thermodynamics of biopolymers II. Correlations between functional groups. Biopolymers 1989;28:1327-1337.
52. Mazur J, Sarai A, Jernigan RL. Sequence dependence of the B-A conformational transition of DNA. Biopolymers 1989;28:1223-1233.
53. Nussinov R, Sarai A, Smythers GW, Wang D, Jernigan RL. Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA. Biochim Biophys Acta 1989;1008:329-338.
54. Covell DG, Jernigan RL. Lattice models of globular proteins. Correlations between sites. International Conference on Supercomputers, Santa Clara, 1989;Vol. II: 357-360.
55. Sarai A, Mazur J, Nussinov R, Jernigan RL. Sequence dependence of DNA conformational flexibility. Biochemistry 1989;28:7842-7849.
56. Nussinov R, Sarai A, Smythers GW, Wang D, Jernigan RL. Strong patterns in homooligomer tract occurrences in non-coding and in potential regulatory sites in eukaryotic genomes. J Biomol Struct Dyn 1989;7:707-722.
57. Jernigan R, Davies D, Scheraga H. Experimental and theoretical protein folding. J Biomol Struct Dyn 1989;6:1039-1043.
58. Mazur J, Sarai A, Jernigan RL. 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 KL, Jernigan RL. Solvent effect on binding thermodynamics of biopolymers. Biopolymers, 1990;29:901-919.
60. Sumner SC, Gallagher KS, Davis DG, Covell DG, Jernigan RL, Ferretti JA. Conformational analysis of the tachykinins in solution: Substance P and physalaemin. J Biomol Struct Dyn 1990;8:687-707.
61. Goodman S, Yang CC, Nash H, Sarai A, Jernigan RL. Bending of DNA by IHF protein. In: RH Sarma and MH Sarma (Eds.) "Structure and Methods: DNA Protein Complexes and Proteins", Vol. 2, Adenine Press, NY, 1990;51-62.
62. Raghunathan G, Jernigan RL, Ting KL, Sarai A. Solvation effects on the sequence variability of DNA double helical conformations. J Biomol Struct Dyn 1990;8:187-198.
63. Jernigan RL. DNA conformational fluctuations. In: R Lavery (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 DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry 1990;29:3287-3294.
65. Jernigan RL, Margalit H, Covell DG. Coarse graining conformations: a peptide binding example. In: DL Beveridge and R Lavery (Eds.) "Theoretical Biochemistry and Molecular Biophysics Vol. 2: Proteins", 1991;69-76.
66. Bohacek RS, Strauss UP, Jernigan RL. Configurational statistics of methyl vinyl ether-maleic anhydride copolymer: selection of important atomic interactions and conformations. Macromolecules 1991;24:731-739.
67. Jernigan RL, Covell DG. Compact protein conformations. In: "Proteins: Structure, Dynamics and Design", ESCOM Science Publishers BV,Leiden, 1991;pp 346-351.
68. Raghunathan G, Jernigan RL, Miles HT, Sasisekharan V. Conformational feasibility of a hairpin with two purines in the loop 5'-d(GGTACIAGTACC-3'. Biochemistry 1991;30:782-788.
69. Zhurkin VB, Ulyanov NB, Gorin AA, Jernigan RL. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc Natl Acad Sci USA 1991;88:7046-7050.
70. Mazur J, Jernigan RL. Distance-dependent dielectric constants and their application to double-helix DNA. Biopolymers 1991;31:1615-1629.
71. Jernigan RL. Generating general shapes and conformations with regular lattices, for compact proteins. In: RH Sarma and MH Sarma (Eds.) "Structure and Function: Proceedings of Seventh Conversation in Biomolecular Stereodynamics", Vol. 2, Adenine Press, 1992;169-182.
72. Jacchieri S, Jernigan RL. Variable ranges of interactions in polypeptide conformations with a method to complement molecular modeling. Biopolymers 1992;32:1327-1388.
73. Sumner SCJ, Jiang SP, Jernigan RL, Ferretti JA. Conformational analysis of receptor selective tachykinin analogs: senktide and septide. J Biomol Struct Dyn 1992;10: 429-439.
74. Jernigan RL. Protein folds. Curr Opin Struct Biol 1992;2:248-256.
75. Olson WK, Marky NL, Jernigan RL, Zhurkin VB. 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, Jernigan RL. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Prot Eng 1993;6:267-278.
77. Jernigan RL, Ting KL. A new approach to protein folding calculations. In: S Doniach (Ed.) "Statistical Mechanics, Protein Structure and Protein Substrate Interactions", Plenum Press, NY, 1994;317-326.
78. Lustig B, Covell D, Jernigan RL. Conformations of t-RNA: Base Pairing and Stacking. J Biomol Struct Dyn, 1994;12:145-161.
79. Young L, Covell D, Jernigan RL. A Role for surface hydrophobicity in protein-protein recognition. Prot Sci 1994;3:717-729.
80. Bahar I, Jernigan RL. Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions. Biophys J 1994;66:454-466.
81. Bahar I, Jernigan RL. Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. Biophys J 1994;66:467-481.
82. Miyazawa S, Jernigan RL. 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 VB, Raghunathan G, Ulyanov NB, Camerini-Otero RD, Jernigan RL. A parallel DNA triplex as a model for the intermediate in homologous recombination. J Mol Biol 1994;239:181-200.
84. Jiang SP, Jernigan RL, Ting KL, Syi JL, Raghunathan G. Stability and Cooperativity of Nucleic Acid Base Triplets. J Biomol Struct Dyn 1994;4:383-399.
85. Zhurkin VB, Raghunathan G, Ulyanov NB, Camerini-Otero RD, Jernigan RL. Recombination triple helix, R-form DNA. A stereochemical model for recognition and strand exchange. in "Structural Biology: State of the Art", Eds. RH Sarma and MH Sarma, Adenine Press, 1994;43-66.
86. Kim MG, Zhurkin VB, Jernigan RL, Camerini-Otero RD. Parallel DNA triplexes and homolgous recombination. in "Structural Biology: State of the Art", Eds. RH Sarma and MH Sarma, Adenine Press, 1994;Vol. II:67-74.
87. Jernigan R, Raghunathan G, Bahar I. Characterization of interactions and metal ion binding sites in proteins. Curr Opin Struct Biol 1994;4:256-263.
88. Jiang SP, Raghunathan G, Ting KL, Xuan JC, Jernigan RL. Geometries, Charges, Dipole Moments and Interaction Energies of Normal, Tautomeric and Novel Bases. J Biomol Struct Dyn 1994;12:367-382
89. Kim MG, Zhurkin VB, Jernigan RL, Camerini-Otero RD. 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, Jernigan RL. Comparison of rotation models for describing DNA conformations: Application to static and polymorphic forms. Biophys J 1995;68:1472-1489.
91. Jernigan RL, Young L, Covell DG, 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 NH, Smith SM, Jernigan RL, Jeang KT. 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 RL, Covell DG. 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, Jernigan RL. Consistencies of individual DNA base-amino acid interactions in structures and sequences. Nucl Acids Res 1995;23:4707-4711.
95. Miyazawa S, Jernigan RL. 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 RL, Sarai A. Constructing optimal backbone segments for joining fixed DNA base pairs. Biophys J 1996;71:1493-1506.
97. Sarai A, Jernigan RL, Mazur J. Interdependence of conformational variables in double helical DNA. Biophys J 1996;71:1507-1518.
98. Bahar I, Jernigan RL. Coordination geometry of non-bonded residues in globular proteins, Folding Des 1996;1:357-370.
99. Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996;6:195-209.
100. Naor D, Fischer D, Jernigan RL, Wolfson HJ, Nussinov R. Amino acid pair interchanges at spatially conserved locations. J Mol Biol 1996; 256:924-938.
101. Teplukhin AV, Zhurkin VB, Jernigan R, Poltev VI. 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 AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins, 1997;29:172-185.
103. Bahar I, Jernigan RL. 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, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins, 1997;29:292-308.
105. Lustig B, Arora S, Jernigan RL. RNA base-amino acid interaction strengths derived from structures and sequences. Nucl Acids Res 1997;25:2562-2565.
106. Erman B, Bahar I, Jernigan RL. Equilibrium states of rigid bodies with multiple interaction sites. Application to protein helices. J Chem Phys 1997;107:2046-2059.
107. Kloczkowski A, Jernigan RL. Efficient method to count and generate compact protein lattice conformations. Macromolecules, 1997;30:6691-6694.
108. Bahar I, Erman B, Haliloglu T, Jernigan RL. Efficient characterization of collective motions and inter-residue correlations in proteins by low resolution simulations. Biochemistry, 1997;36:13512-13523.
109. Raghunathan G, Jernigan RL. Ideal architecture of residue packing and its observation in protein structures. Protein Sci 1997;6:2072-2083, 2485 erratum.
110. Kloczkowski A, Jernigan RL. Computer generation and enumeration of compact self-avoiding walks within simple geometries on lattices. Comput Theoret Polym Sci 1997;7:163-173.
111. Covell DG, Jernigan RL, 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 DG, Jernigan RL. Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry , 1998;37:1067-1075.
113. Jernigan RL. Bahar I. Conformational search: Proteins. In ”The Encyclopedia of Computational Chemistry,” PVR Schleyer, NL Allinger, T Clark; J Gasteiger; PA Kollman; HF Schaefer III; PR Schreiner (Eds.); John Wiley & Sons: Chichester, 1998;562-570.
114. Durell SR, Jernigan RL, Appella E, Nagaich AK, Harrington RE, Zhurkin VB. 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. RH Sarma and MH Sarma (Eds.) New York: Adenine Press, 1998;Vol. 2:277-296.
115. Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB. A role for CH...O interactions in protein-DNA recognition. J Mol Biol 1998;277:1129-1140.
116. Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I. Identification of kinetically hot residues in proteins. Protein Sci 1998;7:2522-2532.
117. Kloczkowski A, Jernigan RL. 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, Jernigan RL. 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. Jernigan RL. 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 AY, Ptitsyn OB, Jernigan RL. 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, Jernigan RL. 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, Jernigan RL. Self-consistent estimation of inter-residue contact energies based on a residue mixture approximation for proteins. Proteins 1999;34:49-68.
123. Bahar I, Erman B, Jernigan RL, Covell DG. Collective motions in HIV-1 reverse transcriptase: Examination of flexibility and enzyme function. J Mol Biol 1999;285:1023-1037.
124. Nagaich AK, Zhurkin VB, Durell SR, Jernigan RL, Appella E, Harrington RE. 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, Jernigan RL. Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition. Proteins 1999;36:347-356.
126. Miyazawa S, Jernigan RL. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999;36:357-369.
127. Bahar I, Jernigan RL. Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry 1999;38:3478-3490.
128. Jernigan RL, Demirel MC, 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, Jernigan RL. Geometric regularities among bonded and non-bonded residues in proteins. In “Perspectives in Structural Biology” (GN Ramachandran Volume) M Vijayan, N Yathindra and AS Kolaskar Eds., Indian Academy of Sciences, Universities Press, Hyderabad, 1999;209-225.
130. Kloczkowski A, Jernigan RL. 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 RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J 2000;78:2093-2106.
132. Keskin O, Bahar I, Jernigan RL, Beutler JA, Shoemaker RH, Sausville EA, Covell DG. 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, Jernigan RL. Identifying sequence-structure pairs undetected by sequence alignments. Prot Eng 2000;13:459-475.
134. Jernigan RL, Bahar I, Covell DG, Atilgan AR, Erman B, Flatow DT. Relating the structure of HIV-1 reverse transcriptase to its processing step. J. Biomol. Struct. Dyn. 2000; Vol.: Conversation 11:49-55.
135. Harrington RE, Zhurkin VB, Durell SR, Jernigan RL, Nagaich AK, Appella EA. Structural model for the p53 Complex with DNA response elements: Implications for p53 function and future research directions. In “Proteome and Protein Analysis”, RM Kamp, D Kyriakidis, and T Choli-Papadopoulou (Eds) Springer-Verlag, Berlin, 2000;257-272.
136. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001;80:505-515.
137. Kloczkowski A, Ting KL, Jernigan RL, Garnier J. Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information. Polymer 2001; 43: 441-449.
138. Tolstorukov MY, Ivanov VI, Malenkov GG, Jernigan RL, Zhurkin VB. Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. Biophys J 2001;81:3409-21.
139. Doruker P, Jernigan RL. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J Comput Chem 2002; 23: 119-27.
140. Manfield ML., Covell D., Jernigan RL. 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 DG, Jernigan RL. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 2002;41:491-501.
142. Ting, KL, Jernigan RL. dentifying a folding nucleus for the lysozyme/alpha-lactalbumin family from sequence conservation clusters. J Mol Evol 2002;54:425-36.
143. Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophys J 2002;83:663-680.
144. Bagci Z, Jernigan RL, Bahar I. Residue packing in proteins: Uniform distribution on a coarse-grained scale. J Chem Phys 2002;116:2269-2276.
145. Kim MK, Jernigan RL, Chirikjian GS. Efficient generation of feasible pathways for protein conformational transitions. Biophys J 2002;83:1620-1630.
146. Kim MK, Jernigan RL, Chirikjian GS. Elastic models of conformational transitions in macromolecules. J Mol Graph Model 2002; 21: 151-160.
147. Doruker P, Jernigan RL, Navizet I, 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 KL, Jernigan RL, Garnier J. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins
2002;49:154-166.
- Kloczkowski A, Jernigan RL. Loop folds in proteins and evolutionary conservation of folding nuclei. J Biomol Struct Dyn 2002;20:323-325.
150. Bagci Z, Jernigan RL, Bahar I. Residue coordination in proteins conforms to the closest packing of spheres. Polymer 2002;43:451-459.
151. Mazur J, Jernigan RL, Sarai A. Conformational effects of stretching DNA. Molec Biol (transl. from Russian) 2003;37:240-249.
152. Bagci Z, Kloczkowski A, Jernigan RL, Bahar I. The origin and extent of coarse-grained regularities in protein internal packing. Proteins -Struct Funct Genet 2003;53:56-67.
153. Kim MK, Jernigan RL, Chirikjian GS. An elastic network model of HK97 capsid maturation.
J Struct Biol 2003;143:107-117.
154. Miyazawa S, Jernigan RL. Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space. Proteins -Struct Funct Genet 2003;50:35-43.
155. Doruker P, Jernigan RL. Functional motions can be extracted from on-lattice construction of protein structures. Proteins 2003;53:174-181.
156. Navizet I, Lavery R, Jernigan RL. Myosin flexibility: Structural domains and collective vibrations. Proteins, 2004;54:384-393.
157. Kloczkowski A, Sen TZ, Jernigan RL. The transfer matrix method for lattice proteins – An application with cooperative interactions. Polymer 2004;45:707-716.
158. Kurkcuoglu O, Jernigan RL, Doruker P. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions. Polymer, 2004;45: 49-657.
159. Kloczkowski A, Jernigan RL. Introduction to “Protein Conformational Computations” - a special issue of Polymer, 2004;45:507.
160. Shchyolkina AK, Kaluzhny DN, Borisova OF, Hawkins ME, Jernigan RL, Jovin TM, Arndt-Jovin DJ, Zhurkin VB. Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin. Nucl Acids Res 2004;32:432-440.
161. Tolstorukov MY, Jernigan RL, Zhurkin VB. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol 2004;337:65-76.
162. Wang Y, Rader AJ, Bahar I, Jernigan RL. Global ribosome motions revealed with elastic network model. J Struct Biol 2004;147:302-314.
163. Kundu S, Jernigan RL. Molecular mechanism of domain swapping in proteins: An analysis of slower motions. Biophys J 2004;86:3846-3854.
164. Sen TZ, Kloczkowski A, Jernigan RL, Yan C, Honavar V, Ho KM, Wang CZ, Ihm Y, Cao H, Gu X, Dobbs D. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods, BMC Bioinformatics 2004;5:205.
165. Kloczkowski A, Sen TZ, Jernigan RL. Promiscuous vs. native protein function. Insights from studying collective motions in proteins by elastic network models, J Biomol Struct Dyn 2005;22: 621-624.
166. Kim MK, Jernigan RL, Chirikjian GS. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies, Biophys J 2005;89:43-55.
167. Pokarowski P, Kloczkowski A, Jernigan RL, Kothari NS, Pokarowska M, Kolinski A. Inferring ideal amino acid interaction forms from statistical protein contact potentials, Proteins: Struct Funct Bioinf 2005;59:49-57.
168. Liao H, Yeh W, Chiang D, Jernigan RL, Lustig B. Protein sequence entropy is closely related to packing density and hydrophobicity. Prot Eng Des Select 2005;18:59-64.
169. Miyazawa S, Jernigan RL. 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.
170. Yan A, Jernigan RL. How do sidechains orient globally in protein structures? Proteins 2005;61:513-522.
171. Cheng H, Sen TZ, Kloczkowski A, Margaritis D, Jernigan RL. Prediction of protein secondary structure by mining structural fragment database, Polymer 2005;46:4314-4321.
172. Sen TZ, Jernigan RL, Garnier J, Kloczkowski. A GOR V server for protein secondary structure prediction, Bioinformatics, 2005;21:2787-2788.
173. Wang Y, Jernigan RL. Comparison of tRNA motions in the free and ribosomal bound structures Biophys J 2005;89:3399-3409.
174. Cui F, Jernigan R, Wu Z. Refinement of NMR-determined protein structures with database derived distance constraints. J Bioinformatics and Comp Biol 2005;3:1315-1329.
175. Kurkcuoglu O, Jernigan RL, Doruker P. Collective dynamics of large proteins from mixed coarse-grained elastic network model. QSAR Comb Sci 2005;24:443-448.
176. Sen TZ, Jernigan RL Optimizing the parameters of the Gaussian network model for ATP-binding proteins, in “Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems,” I Bahar and Q Cui (Eds) Chapman and Hall/CRC, Boca Raton, 2005;171-186.
177. Kurkcuoglu O, Jernigan RL, Doruker P. Loop motions of triosephosphate isomerase observed with elastic networks, Biochemistry, 2006;45:1173-1182.
178. Song G, Jernigan RL. An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins, 2006;63:197-209.
179. Terribilini M, Lee JH, Yan C, Jernigan RL, Honavar V, Dobbs D. (2006). Prediction of protein-RNA interfaces. RNA, 2006;12:1450-1462.
180. Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL. 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.
181. Sen TZ, Kloczkowski A, Jernigan RL. A DNA-centric look at protein-DNA complexes. Structure 2006;14:1341-2.
182. Jernigan RL, Kloczkowski A. Packing regularities in biological structures relate to their dynamics. Methods Mol Biol 2006;350:251-76.
183. Jernigan RL. It was my pleasure to have had Oleg Ptitsyn in my lab. in “Oleg Ptitsyn”, VE Bychkova and AV Finkenstein (Eds Izdatelstvo KDU, Moscow) 2007;149-153.
184. Sen TZ, Kloczkowski A, Jernigan RL. Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics 2006;7:355.
185. 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.
186. 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;15:2499-2506.
187. Terribilini M, Lee JH, Yan C, Jernigan RL, Carpenter S, Honavar V, Dobbs D. Identifying interaction sites in "recalcitrant" proteins: predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data. Pac Symp Biocomp 2006;415-26.
188. Wu D, Cui F, Jernigan R, Wu, ZJ. PIDD: Database for protein inter-atomic distance distributions. Nucl Acids Res 2007;35:D202-D207.
189. Pokarowski P, Kloczkowski A, Nowakowski S, Pokarowska M, Jernigan RL, Kolinski A. Ideal amino acid exchange forms for approximating substitution matrices. Proteins 2007;69:379-393.
190. Peto M, Kloczkowski A, Jernigan RL. Shape-dependent designability studies of lattice proteins. J Phys: Condensed Matter 2007;19:285220 (11 pp).
191. Song G, Jernigan RL. vGNM: a better model for understanding the dynamics of proteins in crystals. J Mol Biol 2007;369:880-893.
192. Wu D, Jernigan R, Wu Z. Refinement of NMR-determined protein structures with database derived mean-force potentials. Proteins 2007;68:232-242.
193. Yang L, Song G, Jernigan RL. How well can we understand large-scale protein motions using elastic normal modes? Biophys J 2007;93:920-929.
194. Feng Y, Kloczkowski A, Jernigan RL. Four-body contact potentials derived from two protein databases to discriminate native structures from decoys. Proteins 2007;68:57-66.
195. Peto M, Sen TZ, Jernigan RL, Kloczkowski A. Generation and enumeration of compact conformations on the 2-dimensional triangular and 3-dimensional fcc lattices. J Chem Phys 2007;127:044101.
196. Terribilini M, Sander JD, Lee J-H, Zaback P, Jernigan RL, Honavar V, Dobbs D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucl Acids Res 2007;35:W578-584.
197. Yan A, Kloczkowski A, Hofmann H, Jernigan RL. Prediction of side chain orientations in proteins by statistical machine learning methods. J Biomol Struct Dyn 2007;25:275-288.
198. Cheng H, Sen TZ, Jernigan RL, Kloczkowski A. Consensus data mining (CDM) protein secondary structure prediction server: Combining GOR V and fragment database mining (FDM). Bioinformatics 2007;23:2628-30.
199. Sułkowska JI, Kloczkowski A, Sen TZ, Cieplak M, Jernigan RL. Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins 2007;71:45-60.
200. Yan C, Wu F, Jernigan RL, Dobbs D, Honavar V. Characterization of protein-protein interfaces. Protein J 2008;27:59-70.
201. Yang L, Song G, Carriquiry A, Jernigan RL. Close Correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure 2008;16:321-330.
202. Jernigan RL, Yang L, Song G, Kurcuoglu O, Doruker P. Elastic network models of coarse-grained proteins are effective for studying the structural control exerted over their dynamics. in “Coarse-Graining of Condensed Phase and Biomolecular Systems” G Voth (Ed) Taylor and Francis Group, LLC, 2008;237-254.
203. Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A. Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA. Biophys J 2008;94:2482-2491.
204. Kloczkowski A, Jernigan RL. Book review of molecular modeling of proteins. Methods in molecular biology, 443. J Amer Chem Soc 2008;130:12548.
205. Feng, Y, Jernigan, RL, Kloczkowski, A. Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron. Proteins 2008;73:730-741.
206. Cui, F, Jernigan, R, Wu, Z. Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement. J Bioinform Comput Biol 2008;6:283-300.
207. Yan A, Wang Y, Kloczkowski A, Jernigan RL. Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome. J Chem Thy Comput 2008;4,1757-1767.
208. Yang, L, Song G, Jernigan RL. Comparisons of experimental and computed protein anisotropic temperature factors. Proteins 2009;76:164-175.
209. Kurcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Phys Biol, 2008;5,46005.
210. Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 2009;75:837-845.
211. Peto M, Kloczkowski A, Honavar V, Jernigan RL. Use of machine learning algorithms to classify binary protein sequences as highly—designable or poorly-designable. BMC Bioinformatics 2008;9:487.
212. Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, Kolinski A, Pokarowski P. Distance matrix-based approach to protein structure prediction. J Struct Funct Genomics 2009;10:67-81.
213. Schuyler, AD, Jernigan RL, Qasba PK, Ramakrishnan B, Chirikjian GS. Iterative cluster-NMA (icNMA): A tool for generating conformational transitions in proteins. Proteins 2009;74:760-776.
214. Yang, L, Song G, Jernigan RL. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci USA 2009;106:12347-12352.
215. Feng Y, Yang L, Kloczkowski A, Jernigan RL. The energy profiles of atomic conformational transition intermediates of adenylate kinase. Proteins 2009;77:551-558.
216. Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophys J, 2009;97:1178-1187.
217. Sun X, Wu D, Jernigan R, Wu Z. PRTAD: A database for protein residue torsion angle distributions. Int J Data Mining Bioinf 2009;3:469-482.
218. Rashin AA, Rashin AHL, Jernigan, RL. Protein flexibility: Coordinate uncertainties and interpretation of structural differences. Acta Crystall 2009;D65:1140-1161.
219. Zimmermann M, Towfic F, Jernigan RL, Kloczkowski A. Short paths in protein structure space originate in graph structure. Proc Natl Acad Sci USA 2009;106:E137.
220. Cui F, Mukhopadhyay K, Young WB, Jernigan RL, Wu Z. Refinement of under-determined loops of human prion protein by database-derived distance constraints. Int J Data Min Bioinf 2009;3:454-68.
221. Katebi A, Kloczkowski A, Jernigan RL. Computational testing of protein-protein interactions, In: Bioinformatics and Biomedicine IEEE International Conference Proceedings, IEEE, New York, 2009;142-149.
222. Feng Y, Kloczkowski A, Jernigan RL. Potentials’R’Us web -server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinformatics 2010;11:92.
223. Cheng H, Sen TZ, Jernigan RL, Kloczkowski A. Data mining for protein secondary structure prediction, In: Data Mining in the Crystallography Issue, D.W.M. Hoffmann and L.N. Kuleshova (Eds), Series: Structure and Bonding Vol. 134, Springer Verlag, Heidelberg, 2010;135-167.
224. Zimmermann MT, Skliros A, Saraswathi S, Kloczkowski A, Jernigan RL. Immunoglobulin functional motions and their effects on the complementarity determining regions, In: “Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology,” (ACM-BCB 2010), Niagara Falls, NY, August 2-4, 2010;621-626.
225. Katebi A, Gniewek P, Zimmermann M, Saraswathi S, Gong Z, Tuggle CK, Kloczkowski A, Jernigan RL. Immunological implications of structural analysis of two different porcine IL1b proteins expressed in macrophages and embryos, In: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010), Niagara Falls, NY, August 2-4, 2010;653-655.
226. Leelananda S, Feng Y, Gniewek P, Kloczkowski A, Jernigan RL. Statistical contact potential in protein coarse-grained modeling: from pair to multi-body potentials. In “Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies” (Ed. A. Kolinski), Springer, Heidelberg, 2011;127-158.
227. Rashin AA, Rashin AH, Jernigan RL. Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity and stability. Biochemistry 2010;49:5683-5704.
228. Katebi AR, Kloczkowski A, Jernigan RL. Structural interpretation of protein-protein interaction network. BMC Struct Biol 2010;10 Suppl 1:S4.
229. Skliros A, Jernigan RL, Kloczkowski A. Models to approximate the motions of protein loops. J Chem Thy Comp, 2010; 6:3249-3258.
230. Long F, Su C-C, Zimmermann MT, Boyken SE, Rajashankar KR, Jernigan RL and Yu EW. Crystal structures of the CusA efflux pump suggest methionine-mediated transport. Nature 2010;467:484-488.
231. Saraswathi S, Kloczkowski A, Jernigan RL. An extreme learning machine classifier for prediction of relative solvent accessibility in proteins. Proceedings of IJCCI/ICNC 2010, ISBN 978-989-8425-32-4: 364-369.
232. Saraswathi S, Jernigan RL, Kloczkowski A. Protein secondary structure prediction using knowledge-based potentials. Proceedings of IJCCI/ICNC 2010, ISBN 978-989-8425-32-4:370-375.
233. Su C-C, Long F, Zimmermann MT, Rajashankar KR, Jernigan RL, Yu EW. Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli. Nature 2011;470:558-62.
234. Huang Y, Bonnet S, Kloczkowski A, Jernigan R, Wu Z. Statistical measures on residue-level protein structural properties. J Struct Funct Genomics 2011;12:119-136.
235. Zimmermann MT, Leelananda SP, Gniewek P, Feng Y , Jernigan RL, Kloczkowski A. Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. J Struct Funct Genomics 2011;12:137-147.
236. Steczkiewicz K, Kurcinski M, Zimmermann MT, Lewis BA, Dobbs DL, Kloczkowski A, Jernigan RL, Kolinski A, Ginalski K. Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step. Proc Natl Acad Sci USA 2011;108:9443-9448.
237. Leelananda S, Towfic F, Jernigan R, Kloczkowski A. Exploration of the relationship between topology and conformations and designability or conformations. J Chem Phys 2011;134:235101 (6 pp).
238. Wu D, Smith S, Mahan H, Jernigan RL, Wu Z. Analysis of protein dynamics using local-DME calculations. Int J Bioinform Res Appl 2011;7:146-161.
239. Zimmermann MT, Kloczkowski A, Jernigan RL. MAVENs: Motion analysis and visualization of elastic networks and structural ensembles. BMC Bioinformatics 2011; 12:264 (7 pp).
240. Fernández-Martínez JL, García-Gonzalo, E, Saraswathi S, Jernigan R, Kloczkowski A. Particle swarm optimization: A powerful family of stochastic optimizers. Analysis, design and application to inverse modelling. Lecture Notes in Computer Science ICSI 2011, Part I, 2011;6728:1-8.
241. Gniewek P, Leelananda SP, Kolinski A, Jernigan RL, Klcozkowski A. Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins 2011;79:1923-1929.
242. Zimmermann MT, Skliros A, Kloczkowski A, Jernigan RL. Immunoglobulin structure exhibits control over CDR motion. Immunome Res 2011; 7:5 (8 pp)
243. Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. How noise in force fields affects the structural refinement of protein models. Proteins, 2011;80:335-341.
244. Fernandez-Martinez JL, Garcia-Gonzalo E, Saraswathi S, Jernigan R, Kloczkowski A. Particle Swarm Optimization: A Powerful Family of Stochastic Optimizers. Analysis, Design and Application to Inverse Modelling. ICSI (Ed. Y Tan et al.), Springer-Verlag, 2011, Lecture Notes in Computer Science 6728 pp 1-8
245. Skliros A, Zimmermann MT, Saraswathi S, Katebi AR, Leelananda SP, Kloczkowski A, Jernigan RL. The importance of slow motions for protein functional loops. Phys Biol 2012;9:014001 (13 pp).
246. Saraswathi S, Fernandez-Martinez JL, Kolinski A, Jernigan RL, Kloczkowski A. Fast learning optimized prediction methodology for protein secondary structure prediction. J Mol Modelling 2012;18:4275-4289.
247. Burton B, Zimmermann MT, Jernigan RL, Wang Y. A Computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. PLoS Comp Biol 2012;8:e1002530 (13 pp).
248. Zimmermann MT, Leelananda SP, Kloczkowski A, Jernigan RL. Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses. J Phys Chem B 2012;116:6725-6731.
249. Zimmermann MT, Jernigan RL. Protein loop dynamics are complex and depend on the motions of the whole protein. Entropy 2012;14,687-700.
250. Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. Elastic network normal modes provide a basis for protein structure refinement. J Chem Phys 2012;136:195101.
251. Huang Y, Bonett S, Kloczkowski A, Jernigan R, Wu Z. P.R.E.S.S. An R-package for exploring residual-level protein structural statistics. J Bioinform Comput Biol. 2012;10:1242007.
252. Gu Y, Sun W, Wang G, Zimmermann MT, Jernigan RL, Fang N. Revealing rotational modes of functional nanoparticles on live cell membranes. Small 2013;9:785-792.
253. Jernigan RL. Possible alternative and extension to the use of dynamics for structure matching. Physics Life Rev 2013;S1571-0645:4-6.
254. Saraswathi S, Fernández-Martínez JL, Koliṅski A, Jernigan RL, Kloczkowski A. Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure. J Mol Model 2013;18:4337-4348.
255. Afonin KA, Wojciech KK, Bindewald E, Puppala PS, Diehl AR, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA. Computational and experimental characterization of RNA cubic nanoscaffolds. Methods 2013; pii: S1046-2023(13)00416-7.
256. Flatow D, Leelananda SP, Skliros A, Kloczkowski A, Jernigan RL. Volumes and surface areas: Geometries and scaling relationships between coarse-grained and atomic structures. Curr Pharm Des. 2014;20:1208-1222.
257. Park JK, Jernigan R, Wu Z. Coarse grained normal mode analysis vs. refined Gaussian network model for protein residue-level structural fluctuations. Bull Math Biol. 2013;75:124-60.
258. Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL. Factors correlating with significant differences between X-ray structures of myoglobin. Acta Crystall D Biol Crystallogr 2014;70 (Pt 2):481-491.
259. Katebi AR, Jernigan RL. The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality . Protein Sci 2014;23:213-228.
260. Zimmermann MT, Yang L, Jernigan RL. Elastic network modes capture the motions apparent within ensembles of RNA structures. RNA, 2014; 20:792-804.
261. Boyken SE, Chopra N, Xie X, Joseph RE, Wales TE, Fulton DB, Engen JR, Jernigan RL, Andreotti A. A conserved isoleucine maintains the inactive state of Bruton's tyrosine kinase. J Mol Biol 2014;426:3656-3669.
262. Katebi A, Sankar K, Jia K, Jernigan RL. The use of experimental structures to model protein dynamics, Chapter 10, in Molecular Modeling of Proteins, Methods in Molecular Biology, Springer 2015;1215:213-236.
263. Jia K, Jernigan RL. Invited Editorial: Combining disparate data types: protein sequences and protein structures. J Data Mining Genomics Proteomics, 2015;6: e117.
264. Katebi AR, Jernigan RL. Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics. Biochemistry. 2015;54:3543-54.
265. Jiang F, An C, Bao Y, Zhao X, Jernigan RL, Lithio A, Nettleton D, Li L, Wurtele ES, Nolan LK, Lu C, Li G. ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli. Infect Immun. 2015;83:3545-54.
266. Sankar K, Liu J, Wang Y, Jernigan, RL. Distributions of Experimental Protein Structures on Coarse-grained Free Energy Landscapes. J Chem Phys. 2015;143:243153.
267. Na H, Jernigan RL, Song G. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. PloS Comput Biol. 2015;11:e1004542.
268. Chopra N, Wales TE, Joseph RE, Boyken SE, Engen JR, Jernigan RL. Andreotti AH. Dynamic allostery mediated by a conserved tryptophan in the Tec family kinases. PLOS Comp Biol 2016;12:e1004826.
269. Zimmermann MT, Jia K, Jernigan RL. Ribosome Mechanics Informs about Mechanism. J Mol Biol. 2016;428 (5 PtA):802-810.
270. Rashin AA, Jernigan RL. Clusters of Structurally Similar MHC I HLA-A2, Found with a New Method, Suggest Mechanisms of T-Cell Receptor Avidity. Biochemistry. 2016;55:167-185.
271. Leelananda SP, Kloczkowski A, Jernigan RL. Fold-Specific Sequence Scoring Improves Protein Sequence Matching. BMC Bioinformatics. 2016;16:328.
272. Leelananda SP, Jernigan RL, Kloczkowski A. Predicting Designability of Small Proteins from Graph Features of Contact Maps. J Comput Biol. 2016;23:400-411
273. Manibog K, Sankar K, Kim SA, Zhang Y, Jernigan RL, Sivasankar S. Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape. Proc Natl Acad Sci U S A. 2016;113,E5711-20.
274. Kandoi G, Leelananda SP, Jernigan RL, Sen, TZ. Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information. Methods Mol Biol. 2017;1484:35-44.
275. Bahar I, Jernigan RL, Dill K. Protein Actions: Principles & Modeling. Garland Science, 2017. 2018 Prose Award Winner for Best New Textbook in the Biological and Life Sciences
276. Sankar K, Jia K, Jernigan, RL. Knowledge-based entropies improve the identification of native protein structures. Proc Natl Acad Sci, USA 2017;114:2928-2933.
277. Mishra SK, Kannan S, Jernigan RL. Altered Dynamics upon Oligomerization Corresponds to Key Functional Sites. Proteins, 2017;85:1422-1434.
278. Liu J, Sankar K, Wang Y, Jia K, Jernigan RL. Directional force originating from ATP hydrolysis drives the GroEL conformational change. Biophys J, 2017;112:1561-1570.
279. Sankar K, Mishra S, Jernigan RL. Comparisons among Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models. J Phys Chem B, 2018;122:5409-5417.
280. Jia K, Jernigan RL. SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence. bioRxiv 2018, 268904.
281. Mishra SK, Jernigan RL. Protein Dynamic Communities from Elastic Network Models Align Closely to the Communities Defined by Molecular Dynamics. PloS One 2018;13:e0199225.
282. Jia M, Mishra S, Tufts S, Jernigan RL, Peters RJ. Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases. Metabolic Eng, 2019:S1096-7176:30141-7.
283. Mishra SK, Kandoi G, Jernigan RL. Coupling Dynamics and Evolutionary Information with Structure to Identify Protein Regulatory and Functional Binding Sites. Proteins, 2019;87:850-868.
284. Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy 2019;21,764 (13 pp).
285. Khade PM, Kumar A, Jernigan RL. Characterizing and Predicting Protein Hinges for Mechanistic Insight. J Mol Biol 2020; 432,508-522.
286. Kono A, Chou T-H, Radhakrishnan A, Bolla J, Sankar K, Shome S, Su CC, Jernigan RL, Robinson CV, Yu EW, Spalding MH. Structure and Function of LCI1: A plasma membrane CO2 channel in the Chlamydomonas CO2 concentrating mechanism. Plant J 2020;102:1107-1126.
287. Scaramozzino D, Khade PM, Jernigan RL, Lacidogna G, Carpinteri A. Structural Compliance – A New Metric for Protein Flexibility. Proteins 2020;88:1482-1492.
288. Jia K., Litterer B.R., Jernigan R.L. Broad Concepts from Polymers applied to Protein Data, in: "Paul Flory's ‘Statistical Mechanics of Chain Molecules’ Today", Alan Tonelli and Gary Patterson, Editors, American Chemical Society Books, 2020;
289. Jia K, Jernigan RL. New amino acid substitution matrix brings sequence alignments into agreement with structure matches. Proteins, 2021:89:671-682.
290. Jernigan, R., Jia, K., Ren, Z., Zhou, W. Large-scale multiple inference of collective dependence with applications to protein function. Annals Appl Statistics, 2021;15:902-924..
291. Jernigan, R.L., Sankar, K., Jia, K., Faraggi, E., and Kloczkowski, A., Computational Ways to Enhance Protein Inhibitor Design, Frontiers in Molecular Biosciences, 7: 607323 (10 pp), 2021.
292. Faraggi E., Jernigan R.L., Kloczkowski A., A Hybrid Levenberg–Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. In: Cartwright H. (Editor) Artificial Neural Networks. Methods in Molecular Biology, vol 2190, pp 307-316, 2021, Humana Press, New York, NY.
293. Jernigan, R.L., Khade, P., Kumar, A., and Kloczkowski, A., Using surface hydrophobicity together with empirical potentials to identify protein-protein binding sites. Application to the interactions of E-cadherins. In: Li, M.S., Kloczkowski, A., Cieplak, M. and Kouza, M., (Eds), Computer Simulations of Aggregation of Proteins and Peptides, (Methods in Molecular Biology, Vol 2340), Springer Nature, New York, 2021, in press
294. Kouza, M., Faraggi, E., Sen. T., Jernigan, R.L., and Kloczkowski, A., Data Mining for Prediction of Protein Structure and Optimization of Protein Crystallizability, in: International Tables for Crystallography, Volume C, 2nd Edition (Richard Wellberry, Editor), International Union of Crystallography, Springer Nature, Switzerland AG, 2020 in press.
295. Ehrlich JJ, Weerts RM, Shome S, Culbertson AT, Honzatko RB, Jernigan RL, Zabotina OA. Xyloglucan xylosyltransferase 1 displays promiscuity toward donor substrates during in vitro reactions, Plant and Cell Physiology, 2021, in press.
296. Kumar A, Jernigan R.L. Ligand Binding Inroduces Significant Allosteric Shifts in the Locations of Protein Fluctuations. Frontiers in Mol Biosciences, 2021, in press.
297. Shome S, Jernigan RL, Beitz DC, Clark S, Testroet ED. Non-Coding RNA in Raw and Commercially Processed Milk and Putative Targets Related to Growth and Immune-Response. BMC Genomics, in press.
298. Khade PM, Scaramozzino D, Kumar A, Lacidogna G, Carpinteri A, Jernigan RL. hdANM: a new comprehensive dynamics model for protein hinges. Biophys J, 2021; online.
299. Shome S, Sankar K, Jernigan RL. Simulated Drug Efflux for the ABGT Family of Membrane Transporters. In press.
Submitted Publications:
Kumar A., Khade PM, Dorman K, Jernigan RL. Coarse-Graining Protein Structures into Their Dynamic Communities with DCI, A Dynamic Community Identifier. Submitted.
Shome S, Anreotti A, Jernigan Robert L. Pathways of multi-drug extrusion through the drug effluex pump HpnN transporter – a member of the RND-family. Submitted.
Khade PM, Jernigan RL. Entropies Derived from the Packing Geometries withn a Single Protein Structure. Submitted.
Khade PM, Jernigan RL PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics. Submitted.