Robert L. Jernigan

47 papers B 1Misc 2Journal 31Unranked 12
YearRankTypeTitle / Venue / Authors
2025 — conf
Seder: Deep Learning Algorithm for Protein Structure Prediction.
IWBBIO (1)
Eshel Faraggi, Robert L. Jernigan, Andrzej Kloczkowski
2024 — conf
Machine Learning-Based Tool for Efficient Discrimination Between Deleterious and Neutral Missense Mutations.
ICAISC (3)
Eshel Faraggi, Robert L. Jernigan, Andrzej Kloczkowski
2023 J jnl
New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions.
Frontiers Bioinform.
Kejue Jia, Mesih Kilinc, Robert L. Jernigan
2023 J jnl
Predicting allosteric pockets in protein biological assemblages.
Bioinform.
Ambuj Kumar, Burak T. Kaynak, Karin S. Dorman, Pemra Doruker, Robert L. Jernigan
2022 J jnl
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier.
Bioinform.
Ambuj Kumar, Pranav M. Khade, Karin S. Dorman, Robert L. Jernigan
2021 — ch.
A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models.
Artificial Neural Networks, 3rd Edition
Eshel Faraggi, Robert L. Jernigan, Andrzej Kloczkowski
2021 J jnl
Simulated Drug Efflux for the AbgT Family of Membrane Transporters.
J. Chem. Inf. Model.
Sayane Shome, Kannan Sankar, Robert L. Jernigan
2019 — conf
Characteristics of Protein Fold Space Exhibits Close Dependence on Domain Usage.
IWBBIO (1)
Michael T. Zimmermann, Fadi Towfic, Robert L. Jernigan, Andrzej Kloczkowski
2019 J jnl
Entropy, Fluctuations, and Disordered Proteins.
Entropy
Eshel Faraggi, A. Keith Dunker, Robert L. Jernigan, Andrzej Kloczkowski
2016 J jnl
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.
PLoS Comput. Biol.
Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, John R. Engen, Robert L. Jernigan, Amy H. Andreotti
2016 J jnl
Fold-specific sequence scoring improves protein sequence matching.
BMC Bioinform.
Sumudu P. Leelananda, Andrzej Kloczkowski, Robert L. Jernigan
2016 J jnl
Predicting Designability of Small Proteins from Graph Features of Contact Maps.
J. Comput. Biol.
Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski
2016 Misc conf
Session Introduction.
PSB
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
2015 J jnl
Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.
PLoS Comput. Biol.
Hyuntae Na, Robert L. Jernigan, Guang Song
2015 B conf
Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models.
RECOMB
Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski
2015 — conf
PRESS-PLOT: An Online Server for Protein Structural Analysis and Evaluation with Residue-level Virtual Angle Correlation Plots.
ISBRA
Yuanyuan Huang, Kejue Jia, Robert L. Jernigan, Zhijun Wu
2014 — conf
An analysis of conformational changes upon RNA-protein binding.
BCB
Kannan Sankar, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
2012 J jnl
A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly.
PLoS Comput. Biol.
Brittany Burton, Michael T. Zimmermann, Robert L. Jernigan, Yongmei Wang
2012 J jnl
P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics.
J. Bioinform. Comput. Biol.
Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu
2012 J jnl
Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein.
Entropy
Michael T. Zimmermann, Robert L. Jernigan
2011 J jnl
Analysis of protein dynamics using local-DME calculations.
Int. J. Bioinform. Res. Appl.
Di Wu, Stephen Smith, Hannah Mahan, Robert L. Jernigan, Zhijun Wu
2011 J jnl
MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles.
BMC Bioinform.
Michael T. Zimmermann, Andrzej Kloczkowski, Robert L. Jernigan
2011 — conf
P.R.E.S.S. - An R-package for exploring residual-level protein structural statistics.
BIBM Workshops
Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu
2011 — conf
Particle Swarm Optimization: A Powerful Family of Stochastic Optimizers. Analysis, Design and Application to Inverse Modelling.
ICSI (1)
Juan Luis Fernández Martínez, Esperanza García Gonzalo, Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski
2010 — conf
An Extreme Learning Machine Classifier for Prediction of Relative Solvent Accessibility in Proteins.
IJCCI (ICFC-ICNC)
Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan
2010 — conf
Immunoglobulin functional motions and their effects on the complementarity determining regions.
BCB
Michael T. Zimmermann, Aris Skliros, Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan
2010 — conf
Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos.
BCB
Ataur R. Katebi, Pawel Gniewek, Michael T. Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher K. Tuggle, Andrzej Kloczkowski, Robert L. Jernigan
2010 J jnl
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials.
BMC Bioinform.
Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan
2010 — conf
Protein Secondary Structure Prediction using Knowledge-based Potentials.
IJCCI (ICFC-ICNC)
Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski, Andrzej Kolinski
2009 J jnl
PRTAD: A database for protein residue torsion angle distributions.
Int. J. Data Min. Bioinform.
Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu
2009 J jnl
Refinement of under-determined loops of Human Prion Protein by database-derived distance constraints.
Int. J. Data Min. Bioinform.
Feng Cui, Kriti Mukhopadhyay, Won-Bin Young, Robert L. Jernigan, Zhijun Wu
2008 J jnl
Knowledge-Based versus experimentally Acquired Distance and Angle Constraints for NMR Structure Refinement.
J. Bioinform. Comput. Biol.
Feng Cui, Robert L. Jernigan, Zhijun Wu
2008 J jnl
Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable.
BMC Bioinform.
Myron Peto, Andrzej Kloczkowski, Vasant G. Honavar, Robert L. Jernigan
2007 J jnl
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM).
Bioinform.
Haitao Cheng, Taner Z. Sen, Robert L. Jernigan, Andrzej Kloczkowski
2007 J jnl
PIDD: database for Protein Inter-atomic Distance Distributions.
Nucleic Acids Res.
Di Wu, Feng Cui, Robert L. Jernigan, Zhijun Wu
2007 J jnl
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.
Nucleic Acids Res.
Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
2006 J jnl
Functional clustering of yeast proteins from the protein-protein interaction network.
BMC Bioinform.
Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan
2006 Misc conf
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
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter
2006 J jnl
Predicting DNA-binding sites of proteins from amino acid sequence.
BMC Bioinform.
Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant G. Honavar
2005 J jnl
GOR V server for protein secondary structure prediction.
Bioinform.
Taner Z. Sen, Robert L. Jernigan, Jean Garnier, Andrzej Kloczkowski
2005 J jnl
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
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter, Vasant G. Honavar, Drena Dobbs
2005 J jnl
Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints.
J. Bioinform. Comput. Biol.
Feng Cui, Robert L. Jernigan, Zhijun Wu
2004 J jnl
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.
BMC Bioinform.
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
2003 — conf
A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method.
METMBS
Moon K. Kim, Robert L. Jernigan, Bruce A. Shapiro, Gregory S. Chirikjian
2002 J jnl
A New Class of Molecular Shape Descriptors, 1. Theory and Properties.
J. Chem. Inf. Comput. Sci.
Marc L. Mansfield, David G. Covell, Robert L. Jernigan
2002 J jnl
Dynamics of large proteins through hierarchical levels of coarse-grained structures.
J. Comput. Chem.
Pemra Doruker, Robert L. Jernigan, Ivet Bahar
1997 J jnl
RNA base-amino acid interaction strengths derived from structures and sequences.
Nucleic Acids Res.
Brooke Lustig, Shalini Arora, Robert L. Jernigan