Robert L. Jernigan

Publication Activity (10 Years)

Years Active: 1997-2023
Publications (10 Years): 13

Top Topics

Biological Knowledge

Protein Sequences

Top Venues

PLoS Comput. Biol.

J. Comput. Biol.

Publications

Kejue Jia, Mesih Kilinc, Robert L. Jernigan
New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions. Frontiers Bioinform. 3 (2023)
Ambuj Kumar, Burak T. Kaynak, Karin S. Dorman, Pemra Doruker, Robert L. Jernigan
Predicting allosteric pockets in protein biological assemblages. Bioinform. 39 (5) (2023)
Ambuj Kumar, Pranav M. Khade, Karin S. Dorman, Robert L. Jernigan
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier. Bioinform. 38 (10) (2022)
Sayane Shome, Kannan Sankar, Robert L. Jernigan
Simulated Drug Efflux for the AbgT Family of Membrane Transporters. J. Chem. Inf. Model. 61 (11) (2021)
Michael T. Zimmermann, Fadi Towfic, Robert L. Jernigan, Andrzej Kloczkowski
Characteristics of Protein Fold Space Exhibits Close Dependence on Domain Usage. IWBBIO (1) (2019)
Eshel Faraggi, A. Keith Dunker, Robert L. Jernigan, Andrzej Kloczkowski
Entropy, Fluctuations, and Disordered Proteins. Entropy 21 (8) (2019)
Sumudu P. Leelananda, Andrzej Kloczkowski, Robert L. Jernigan
Fold-specific sequence scoring improves protein sequence matching. BMC Bioinform. 17 (2016)
Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, John R. Engen, Robert L. Jernigan, Amy H. Andreotti
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases. PLoS Comput. Biol. 12 (3) (2016)
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
Session Introduction. PSB (2016)
Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski
Predicting Designability of Small Proteins from Graph Features of Contact Maps. J. Comput. Biol. 23 (5) (2016)
Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski
Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models. RECOMB (2015)
Yuanyuan Huang, Kejue Jia, Robert L. Jernigan, Zhijun Wu
PRESS-PLOT: An Online Server for Protein Structural Analysis and Evaluation with Residue-level Virtual Angle Correlation Plots. ISBRA (2015)
Hyuntae Na, Robert L. Jernigan, Guang Song
Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. PLoS Comput. Biol. 11 (10) (2015)
Kannan Sankar, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
An analysis of conformational changes upon RNA-protein binding. BCB (2014)
Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu
P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics. J. Bioinform. Comput. Biol. 10 (3) (2012)
Brittany Burton, Michael T. Zimmermann, Robert L. Jernigan, Yongmei Wang
A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly. PLoS Comput. Biol. 8 (5) (2012)
Michael T. Zimmermann, Robert L. Jernigan
Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein. Entropy 14 (4) (2012)
Juan Luis Fernández Martínez, Esperanza García Gonzalo, Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski
Particle Swarm Optimization: A Powerful Family of Stochastic Optimizers. Analysis, Design and Application to Inverse Modelling. ICSI (1) (2011)
Michael T. Zimmermann, Andrzej Kloczkowski, Robert L. Jernigan
MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles. BMC Bioinform. 12 (2011)
Di Wu, Stephen Smith, Hannah Mahan, Robert L. Jernigan, Zhijun Wu
Analysis of protein dynamics using local-DME calculations. Int. J. Bioinform. Res. Appl. 7 (2) (2011)
Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu
P.R.E.S.S. - An R-package for exploring residual-level protein structural statistics. BIBM Workshops (2011)
Ataur R. Katebi, Pawel Gniewek, Michael T. Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher K. Tuggle, Andrzej Kloczkowski, Robert L. Jernigan
Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos. BCB (2010)
Michael T. Zimmermann, Aris Skliros, Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan
Immunoglobulin functional motions and their effects on the complementarity determining regions. BCB (2010)
Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinform. 11 (2010)
Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan
An Extreme Learning Machine Classifier for Prediction of Relative Solvent Accessibility in Proteins. IJCCI (ICFC-ICNC) (2010)
Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski, Andrzej Kolinski
Protein Secondary Structure Prediction using Knowledge-based Potentials. IJCCI (ICFC-ICNC) (2010)
Feng Cui, Kriti Mukhopadhyay, Won-Bin Young, Robert L. Jernigan, Zhijun Wu
Refinement of under-determined loops of Human Prion Protein by database-derived distance constraints. Int. J. Data Min. Bioinform. 3 (4) (2009)
Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu
PRTAD: A database for protein residue torsion angle distributions. Int. J. Data Min. Bioinform. 3 (4) (2009)
Feng Cui, Robert L. Jernigan, Zhijun Wu
Knowledge-Based versus experimentally Acquired Distance and Angle Constraints for NMR Structure Refinement. J. Bioinform. Comput. Biol. 6 (2) (2008)
Myron Peto, Andrzej Kloczkowski, Vasant G. Honavar, Robert L. Jernigan
Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. BMC Bioinform. 9 (2008)
Di Wu, Feng Cui, Robert L. Jernigan, Zhijun Wu
PIDD: database for Protein Inter-atomic Distance Distributions. Nucleic Acids Res. 35 (Database-Issue) (2007)
Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Haitao Cheng, Taner Z. Sen, Robert L. Jernigan, Andrzej Kloczkowski
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). Bioinform. 23 (19) (2007)
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter
Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data. Pacific Symposium on Biocomputing (2006)
Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant G. Honavar
Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinform. 7 (2006)
Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan
Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinform. 7 (2006)
Taner Z. Sen, Robert L. Jernigan, Jean Garnier, Andrzej Kloczkowski
GOR V server for protein secondary structure prediction. Bioinform. 21 (11) (2005)
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter, Vasant G. Honavar, Drena Dobbs
Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and Rna Binding Sites in Rev Proteins of Hiv-1 and Eiav Agree with Experimental Data CoRR (2005)
Feng Cui, Robert L. Jernigan, Zhijun Wu
Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints. J. Bioinform. Comput. Biol. 3 (6) (2005)
Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant G. Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinform. 5 (2004)
Moon K. Kim, Robert L. Jernigan, Bruce A. Shapiro, Gregory S. Chirikjian
A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method. METMBS (2003)
Marc L. Mansfield, David G. Covell, Robert L. Jernigan
A New Class of Molecular Shape Descriptors, 1. Theory and Properties. J. Chem. Inf. Comput. Sci. 42 (2) (2002)
Pemra Doruker, Robert L. Jernigan, Ivet Bahar
Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23 (1) (2002)
Brooke Lustig, Shalini Arora, Robert L. Jernigan
RNA base-amino acid interaction strengths derived from structures and sequences. Nucleic Acids Res. 25 (13) (1997)