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Robert Jernigan
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Professor of Biochemistry, Biophysics and Molecular Biology
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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
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Articles
(203)
Article
Refinement of Under-Determined Loops of Human Prion Protein by Database-Derived ...
International journal of data mining and bioinformatics (2009)
Feng Cui, Kriti Mukhopadhyay, Won-Bin Young, Robert L. Jernigan, et al.
Computational simulations of the conversion from the normal cellular prion (PrPc) to the scrapie prion (PrPSc) are usually based on ...
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Article
The ribosome structure controls and directs mRNA entry, translocation and ...
Physical Biology (2008)
Ozge Kurkcuoglu, Pemra Doruker, Taner Z. Sen, Andrzej Kloczkowski, et al.
The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here the domain motions of this ...
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Article
Orientational distributions of contact clusters in proteins closely resemble those ...
Proteins: Structure, Function, and Bioinformatics (2008)
Yaping Feng, Robert L. Jernigan and Andrzej Kloczkowski
The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with ...
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Article
Predicting the order in which contacts are broken during single ...
Proteins: Structure, Function, and Bioinformatics (2008)
Joanna I. Sulkowska, Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak, et al.
We combine two methods to enable the prediction of the order in which contacts are broken under external stretching forces ...
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Article
Close Correspondence between the Motions from Principal Component Analysis of ...
Structure (2008)
Lei Yang, Guang Song, Alicia L. Carriquiry and Robert L. Jernigan
The large number of available HIV-1 protease structures provides a remarkable sampling of conformations of the different conformational states, which ...
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Article
Characterization of Protein–Protein Interfaces
The Protein Journal (2008)
Changhui Yan, Feihong Wu, Robert L. Jernigan, Drena Dobbs, et al.
We analyze the characteristics of protein–protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start ...
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Article
Effects of Protein Subunits Removal on the Computed Motions of ...
Journal of Chemical Theory and Computation (2008)
Aimin Yan, Yongmei Wang, Andrzej Kloczkowski and Robert L. Jernigan
The Anisotropic Network Model (ANM) is used to study motions of the 30S small ribosomal subunit. The effect of the ...
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Article
Knowledge-based versus experimentally acquired distance and angle constraints for NMR ...
Journal of Bioinformatics and Computational Biology (2008)
Feng Cui, Robert Jernigan and Zhijun Wu
Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure ...
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Article
Use of machine learning algorithms to classify binary protein sequences ...
BMC Bioinformatics (2008)
Myron Peto, Andrzej Kloczkowski, Vasant Honavar and Robert L. Jernigan
Background By using a standard Support Vector Machine (SVM) with a Sequential Minimal Optimization (SMO) method of training, Naïve Bayes ...
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Article
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining ...
Bioinformatics (2007)
Haitao Cheng, Taner Z. Sen, Robert L. Jernigan and Andrzej Kloczkowski
One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we ...
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Article
Shape-dependent designability studies of lattice proteins
Journal of Physics: Condensed Matter (2007)
Myron Peto, Andrzej Kloczkowski and Robert L. Jernigan
One important problem in computational structural biology is protein designability, that is, why protein sequences are not random strings of ...
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Article
vGNM: a Better Model for Understanding the Dynamics of Proteins ...
Journal of Molecular Biology (2007)
Guang Song and Robert L. Jernigan
The dynamics of proteins are important for understanding their functions. In recent years, the simple coarse-grained Gaussian Network Model (GNM) ...
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Article
Generation and enumeration of compact conformations on the two-dimensional triangular ...
The Journal of Chemical Physics (2007)
Myron Peto, Taner Z. Sen, Robert L. Jernigan and Andrzej Kloczkowski
We enumerated all compact conformations within simple geometries on the two-dimensional (2D) triangular and three-dimensional (3D) face centered cubic (fcc) ...
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Article
PIDD: database for Protein Inter-atomic Distance Distributions
Nucleic Acids Research (2007)
Di Wu, Robert Jernigan and Zhijun Wu
Protein Inter-atomic Distance Distributions (PIDD) is a dedicated database and structural bio-informatics system for distance based protein modeling. The database ...
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Article
RNABindR: a server for analyzing and predicting RNA-binding sites in ...
Nucleic Acids Research (2007)
Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, et al.
Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe ...
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Article
Functional clustering of yeast proteins from the protein-protein interaction network
BMC Bioinformatics (2006)
Taner Z. Sen, Andrzej Kloczkowski and Robert L. Jernigan
Background The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are ...
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Article
Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks
Biochemistry (2006)
Ozge Kurkcuoglu, Robert L. Jernigan and Pemra Doruker
The internal dynamics of triosephosphate isomerase have been investigated with elastic networks, with and without a substrate bound. The slowest ...
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Article
Predicting DNA-binding sites of proteins from amino acid sequence
BMC Bioinformatics (2006)
Changhui Yan, Michael Terribilini, Feihong Wu, Robert L Jernigan, et al.
Background Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a ...
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Article
Prediction of RNA binding sites in proteins from amino acid ...
RNA (2006)
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, et al.
RNA–protein interactions are vitally important in a wide range of biological processes, including regulation of gene expression, protein synthesis, and ...
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Article
The Extent of Cooperativity of Protein Motions Observed with Elastic ...
Journal of Chemical Theory and Computation (2006)
Taner Z. Sen, Yaping Feng, John V. Garcia, Andrzej Kloczkowski, et al.
Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually ...
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Article
How Do Side Chains Orient Globally in Protein Structures?
Proteins: Structure, Function, and Bioinformatics (2005)
Aimin Yan and Robert L. Jernigan
An angle Ω is defined to serve as a metric for global side-chain orientations, which reflects the orientation of the ...
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Article
GOR V server for protein secondary structure prediction
Bioinformatics (2005)
Taner Z. Sen, Robert L. Jernigan, Jean Garnier and Andrzej Kloczkowski
We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, ...
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Article
Prediction of protein secondary structure by mining structural fragment database
Polymer (2005)
Haitao Cheng, Taner Z. Sen, Andrzej Kloczkowski, Dimitris Margaritis, et al.
A new method for predicting protein secondary structure from amino acid sequence has been developed. The method is based on ...
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Article
Inferring Ideal Amino Acid Interaction Forms From Statistical Protein Contact ...
Proteins: Structure, Function, and Bioinformatics (2005)
Piotr Pokarowski, Andrzej Kloczkowski, Robert L. Jernigan, Neha S. Kothari, et al.
We have analyzed 29 different published matrices of protein pairwise contact potentials (CPs) between amino acids derived from different sets ...
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Article
Protein sequence entropy is closely related to packing density and ...
Protein Engineering, Design and Selection (2005)
H. Liao, W. Yeh, D. Chiang, Robert L. Jernigan, et al.
We investigated the correlation between the Shannon information entropy, ‘sequence entropy’, with respect to the local flexibility of native globular ...
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