Skip to main content
SelectedWorks
MENU
Toggle navigation menu
Sign up
Log in
Learn about SelectedWorks
Follow
Contact
Selected Works of
Robert Jernigan
Selected Works of
Save
Cancel
Professor of Biochemistry, Biophysics and Molecular Biology
Title
Save
Cancel
read more
Works
About
×
About Robert Jernigan
Positions
Present
Professor of Biochemistry, Biophysics and Molecular Biology,
Iowa State University
Institution
Organization
Position Type
Position Title
Time Period
to
Options
Current Position
Affiliate my profile with this Institution
Save
Cancel
Disciplines
Biochemistry, Biophysics, and Structural Biology
Title
URL
Funding Agency
Grant Name
Grant Number
Amount
$
Role
Colleague(s)
Time Period
to
Enter a valid date range.
Current Grant
Save
Cancel
Position
Affiliation
Time Period
to
Enter a valid date range.
Current Position
URL
Save
Cancel
Jump to Category
View All
Articles
Book Chapters
Conference Proceedings
Reports
Articles
(203)
Article
Non-Coding RNA in Raw and Commercially Processed Milk and Putative ...
Food Science and Human Nutrition Publications (2020)
Sayane Shome, Robert Jernigan, Donald C. Beitz, Stephanie Clark, et al.
Background: Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, ...
Download
Article
Characterizing and Predicting Protein Hinges for Mechanistic Insight
Journal of Molecular Biology (2019)
Pranav M. Khade, Ambuj Kumar and Robert L. Jernigan
The functioning of proteins requires highly specific dynamics, which depend critically on the details of how amino acids are packed. ...
Download
Article
Combinatorial biosynthesis and the basis for substrate promiscuity in class ...
Metabolic Engineering (2019)
Meirong Jia, Sambit K. Mishra, Samuel Tufts, Robert L. Jernigan, et al.
Terpene synthases are capable of mediating complex reactions, but fundamentally simply catalyze lysis of allylic diphosphate esters with subsequent deprotonation. ...
Download
Article
Coupling Dynamics and Evolutionary Information with Structure to Identify Protein ...
Proteins (2019)
Sambit Kumar Mishra, Gaurav Kandoi and Robert L. Jernigan
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity ...
Download
Article
Entropy, Fluctuations, and Disordered Proteins
Entropy (2019)
Eshel Faraggi, A. Keith Dunker, Robert L. Jernigan and Andrzej Kloczkowski
Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of ...
Download
Article
Protein dynamic communities from elastic network models align closely to ...
PloS ONE (2018)
Sambit Kumar Mishra and Robert L. Jernigan
Dynamic communities in proteins comprise the cohesive structural units that individually exhibit rigid body motions. These can correspond to structural ...
Download
Article
SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence ...
bioRxiv (2018)
Kejue Jia and Robert L. Jernigan
Protein sequence matching does not properly account for some well-known features of protein structures: surface residues being more variable than ...
Download
Article
Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics ...
The Journal of Physical Chemistry B (2018)
Kannan Sankar, Sambit K. Mishra and Robert L. Jernigan
Predicting protein motions is important for bridging the gap between protein structure and function. With growing numbers of structures of ...
Download
Article
Altered dynamics upon oligomerization corresponds to key functional sites
Proteins: Structure, Function, and Bioinformatics (2017)
Sambit Kumar Mishra, Kannan Sankar and Robert L. Jernigan
It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural ...
Download
Article
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec ...
PLOS Computational Biology (2016)
Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, et al.
Bruton’s tyrosine kinase (Btk) is a Tec family non-receptor tyrosine kinase that plays a critical role in immune signaling and ...
Download
Article
Ribosome Mechanics Informs about Mechanism
Journal of Molecular Biology (2016)
Michael T. Zimmermann, Kejue Jia and Robert L. Jernigan
The essential aspects of the ribosome’s mechanism can be extracted from coarse-grained simulations, including the ratchet motion, the movement together ...
Download
Article
Distributions of experimental protein structures on coarse-grained free energy landscapes
The Journal of Chemical Physics (2016)
Kannan Sankar, Jie Liu, Yuan Wang and Robert L. Jernigan
Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available ...
Download
Article
Fold-specific sequence scoring improves protein sequence matching
BMC Bioinformatics (2016)
Sumudu P. Leelananda, Andrzej Kloczkowski and Robert L. Jernigan
Background Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, ...
Download
Article
Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy ...
PLOS Computational Biology (2015)
Hyuntae Na, Robert L. Jernigan and Guang Song
Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as ...
Download
Article
Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics
Biochemistry (2015)
Ataur R. Katebi and Robert L. Jernigan
Aldolases are essential enzymes in the glycolysis pathway and catalyze the reaction cleaving fructose/tagatose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde ...
Download
Article
ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity ...
Infection and Immunity (2015)
Fengwei Jiang, Chunxia An, Yinli Bao, Xuefeng Zhao, et al.
Avian pathogenic Escherichia coli (APEC) strains cause one of the three most significant infectious diseases in the poultry industry and ...
Download
Article
Combining Disparate Data Types: Protein Sequences and Protein Structures
Journal of Data Mining in Genomics & Proteomics (2015)
Kejue Jia and Robert L. Jernigan
With the development of high-throughput, next-generation sequencing and other advanced technologies, a large number of gene expression profiles have been ...
Download
Article
A conserved isoleucine maintains the inactive state of Bruton’s ...
Journal of Molecular Biology (2014)
Scott E. Boyken, Nikita Chopra, Qian Xie, Raji E. Joseph, et al.
Despite high homology among non-receptor tyrosine kinases, different kinase families employ a diverse array of regulatory mechanisms. For example, the ...
Download
Article
Computational and Experimental Characterization of RNA Cubic Nanoscaffolds
Methods (2014)
Kirill A Afonin, Wojciech K Kasprzak, Eckart Bindewald, Praneet S Puppala, et al.
The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and ...
Download
Article
Factors correlating with significant differences between X-ray structures of myoglobin
Acta Crystallographica Section D (2014)
Alexander A Rashin, Marcin J Domagalski, Michael T Zimmermann, Wladek Minor, et al.
Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful ...
Download
Article
Elastic network models capture the motions apparent within ensembles of ...
RNA (2014)
Michael T. Zimmermann and Robert L. Jernigan
The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have ...
Download
Article
Distributions of amino acids suggest that certain residue types more ...
Journal of Molecular Modeling (2013)
S. Saraswathi Battelle, J .L. Fernández-Martínez, A. Koliński, R. L. Jernigan, et al.
Exponential growth in the number of available protein sequences is unmatched by the slower growth in the number of structures. ...
Download
Article
Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model ...
Bulletin of Mathematical Biology (2013)
Jun-Koo Park, Robert Jernigan and Zhijun Wu
We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of ...
Download
Article
Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure ...
Journal of Molecular Modeling (2012)
Saras Saraswathi, Juan Luis Fernandez-Martinez, Andrzej Kolinski, Robert L. Jernigan, et al.
Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome ...
Download
Article
P.R.E.S.S. – An R-package for Exploring Residual-Level ...
Journal of Bioinformatics and Computational Biology (2012)
Yuanyuan Huang, Steve Bonett, Andrzej Klockowski, Robert Jernigan, et al.
P.R.E.S.S. is an R package developed to allow researchers to get access to and manipulate on a large set of ...
Download
More