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Robert Jernigan
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Professor of Biochemistry, Biophysics and Molecular Biology
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About Robert Jernigan
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Professor of Biochemistry, Biophysics and Molecular Biology,
Iowa State University
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Biochemistry, Biophysics, and Structural Biology
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Articles
Book Chapters
Conference Proceedings
Reports
Articles
(203)
Article
How effective for fold recognition is a potential of mean ...
The Journal of Chemical Physics (2005)
Sanzo Miyazawa and Robert L. Jernigan
We estimate the statistical distribution of relative orientations between contacting residues from a database of protein structures and evaluate the ...
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Article
Protein Promiscuity: Drug Resistance and Native Functions—HIV-1 Case
Journal of Biomolecular Structure and Dynamics (2005)
Ariel Fernandez, Dan S. Tawfik, Ben Berkhout, Rogier W. Sanders, et al.
The association of a drug with its target protein has the effect of blocking the protein activity and is termed ...
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Article
Protein–DNA Hydrophobic Recognition in the Minor Groove is Facilitated ...
Journal of Molecular Biology (2004)
Michael Y. Tolstorukov, Robert L. Jernigan and Victor B. Zhurkin
Information readout in the DNA minor groove is accompanied by substantial DNA deformations, such as sugar switching between the two ...
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Article
Myosin flexibility: Structural domains and collective vibrations
Proteins (2004)
Isabelle Navizet, Richard Lavery and Robert L. Jernigan
The movement of the myosin motor along an actin filament involves a directed conformational change within the cross-bridge formed between ...
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Article
Formation of an intramolecular triple‐stranded DNA structure monitored by ...
Nucleic Acids Research (2004)
Anna K. Shchyolkina, Dmitry N. Kaluzhny, Olga F. Borisova, Mary E. Hawkins, et al.
The parallel (recombination) ‘R‐triplex’ can accommodate any nucleotide sequence with the two identical DNA strands in parallel orientation. We have ...
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Article
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods
BMC Bioinformatics (2004)
Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, et al.
Background Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major ...
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Article
Conformational Effects of DNA Stretching
Molecular Biology (2003)
J. Mazur, R. L. Jernigan and A Sarai
DNA is an extensible molecule, and an extended conformation of DNA is involved in some biological processes. We have examined ...
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Article
Long- and short-range interactions in native protein structures are consistent ...
Proteins (2003)
Sanzo Miyazawa and Robert L. Jernigan
We show that long- and short-range interactions in almost all protein native structures are actually consistent with each other for ...
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Article
Combining the GOR V algorithm with evolutionary information for protein ...
Proteins (2002)
A. Kloczkowski, K.-L. Ting, R. L. Jernigan and J. Garnier
We have modified and improved the GOR algorithm for the protein secondary structure prediction by using the evolutionary information provided ...
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Article
Elastic models of conformational transitions in macromolecules
Journal of Molecular Graphics and Modeling (2002)
Moon K Kim, Gregory S Chirikjian and Robert L Jernigan
We develop a computationally efficient and physically realistic method to simulate the transition of a macromolecule between two conformations. Our ...
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Article
Efficient Generation of Feasible Pathways for Protein Conformational Transitions
Biophysical Journal (2002)
Moon K Kim, Robert L Jernigan and Gregory S Chirikjian
We develop a computationally efficient method to simulate the transition of a protein between two conformations. Our method is based ...
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Article
Relating Molecular Flexibility to Function: A Case Study of Tubulin
Biophysical journal (2002)
Ozlem Keskin, Stewart R. Durell, Ivet Bahar, Robert L. Jernigan, et al.
Microtubules (MT), along with a variety of associated motor proteins, are involved in a range of cellular functions including vesicle ...
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Article
Identifying a Folding Nucleus for the Lysozyme/α-Lactalbumin Family from ...
Journal of Molecular Evolution (2002)
Kai-Li H. Ting and Robert L. Jernigan
Four subfamilies of c-type lysozyme and one subfamily of α-lactalbumin are defined from 78 sequences, and their folding nucleus is identified ...
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Article
Residue packing in proteins: Uniform distribution on a coarse-grained scale
The Journal of Chemical Physics (2002)
Zerrin Bagci, Robert L. Jernigan and Ivet Bahar
The high packing density of residues in proteins ought to be manifested in some order; to date this packing order has not ...
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Article
Dynamics of large proteins through hierarchical levels of coarse-grained structures
Journal of computational chemistry (2002)
Pemra Doruker, Robert L. Jernigan and Ivet Bahar
Elastic network models have been successful in elucidating the largest scale collective motions of proteins. These models are based on ...
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Article
A New Class of Molecular Shape Descriptors. 1. Theory and ...
Journal of chemical information and computer sciences (2002)
Marc L. Mansfield, David G. Covell and Robert L. Jernigan
The integrals V (n1, n2, n3) = ∫ dr xn1 yn2 zn3, where ∫ dr represents integration over the volume of a body, such as a molecule, where x, y, and z are Cartesian ...
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Article
Important fluctuation dynamics of large protein structures are preserved upon ...
International Journal of Quantum Chemistry (2002)
Pemra Doruker, Robert L Jernigan, Isabelle Navizet and Rigoberto Hernandez
The fluctuations and important motions of three large proteins—hemaglutinin, xanthine dehydrogenase, and β-galactosidase—have been considered with a range of models ...
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Article
Molecular Mechanisms of Chaperonin GroEL−GroES Function
Biochemistry (2002)
O. Keskin, I. Bahar, D. Flatow, D. G. Covell, et al.
The dynamics of the GroEL−GroES complex is investigated with a coarse-grained model. This model is one in which single-residue points ...
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Article
Protein secondary structure prediction based on the GOR algorithm incorporating ...
Polymer (2002)
A. Kloczkowski, K.-L. Ting, R. L. Jernigan and J. Garnier
We have developed a new method for the prediction of the protein secondary structure from the amino acid sequence. The ...
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Article
Residue coordination in proteins conforms to the closest packing of ...
Polymer (2002)
Zerrin Bagci, Robert L. Jernigan and Ivet Bahar
Coarse-grained protein structures have the unusual property of manifesting a greater regularity than is evident when all atoms are considered. ...
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Article
Sequence-Dependent B↔A Transition in DNA Evaluated with Dimeric and ...
Biophysical journal (2001)
M. Y. Tolstorukov, V. I. Ivanov, G. G. Malenkov, R. L. Jernigan, et al.
Experimental data on the sequence-dependent B↔A conformational transition in 24 oligo- and polymeric duplexes yield optimal dimeric and trimeric scales ...
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Article
Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network ...
Biophysical journal (2001)
A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, et al.
Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which ...
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Article
Identifying sequence–structure pairs undetected by sequence alignments
Protein Engineering (2000)
Sanzo Miyazawa and Robert L. Jernigan
We examine how effectively simple potential functions previously developed can identify compatibilities between sequences and structures of proteins for database ...
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Article
Characterization of anticancer agents by their growth inhibitory activity and ...
Anti-Cancer Drug Design (2000)
Ozlem Keskin, Ivet Bahar, Robert L. Jernigan, John A. Beutler, et al.
An analysis of the growth inhibitory potency of 122 anticancer agents available from the National Cancer Institute anticancer drug screen ...
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Article
Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior
Biophysical Journal (2000)
O. Keskin, R. L. Jernigan and I. Bahar
We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold ...
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