RNA base-amino acid interaction strengths derived from structures and sequences. - Brooke Lustig; Shalini Arora; Robert L. Jernigan (Nucleic Acids Res., 1997)

Dynamics of large proteins through hierarchical levels of coarse-grained structures. - Pemra Doruker; Robert L. Jernigan; Ivet Bahar (J. Comput. Chem., 2002)

A New Class of Molecular Shape Descriptors, 1. Theory and Properties. - Marc L. Mansfield; David G. Covell; Robert L. Jernigan (J. Chem. Inf. Comput. Sci., 2002)

A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method. - Moon K. Kim; Robert L. Jernigan; Bruce A. Shapiro; Gregory S. Chirikjian (METMBS, 2003)

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. - 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 (BMC Bioinform., 2004)

GOR V server for protein secondary structure prediction. - Taner Z. Sen; Robert L. Jernigan; Jean Garnier; Andrzej Kloczkowski (Bioinform., 2005)

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and Rna Binding Sites in Rev Proteins of Hiv-1 and Eiav Agree with Experimental Data - Michael Terribilini; Jae-Hyung Lee; Changhui Yan; Robert L. Jernigan; Susan Carpenter; Vasant G. Honavar; Drena Dobbs (CoRR, 2005)

Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints. - Feng Cui; Robert L. Jernigan; Zhijun Wu (J. Bioinform. Comput. Biol., 2005)

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data. - Michael Terribilini; Jae-Hyung Lee; Changhui Yan; Robert L. Jernigan; Susan Carpenter (Pacific Symposium on Biocomputing, 2006)

Functional clustering of yeast proteins from the protein-protein interaction network. - Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2006)

Predicting DNA-binding sites of proteins from amino acid sequence. - Changhui Yan; Michael Terribilini; Feihong Wu; Robert L. Jernigan; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2006)

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). - Haitao Cheng; Taner Z. Sen; Robert L. Jernigan; Andrzej Kloczkowski (Bioinform., 2007)

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. - Michael Terribilini; Jeffry D. Sander; Jae-Hyung Lee; Peter Zaback; Robert L. Jernigan; Vasant G. Honavar; Drena Dobbs (Nucleic Acids Res., 2007)

PIDD: database for Protein Inter-atomic Distance Distributions. - Di Wu; Feng Cui; Robert L. Jernigan; Zhijun Wu (Nucleic Acids Res., 2007)

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. - Myron Peto; Andrzej Kloczkowski; Vasant G. Honavar; Robert L. Jernigan (BMC Bioinform., 2008)

Knowledge-Based versus experimentally Acquired Distance and Angle Constraints for NMR Structure Refinement. - Feng Cui; Robert L. Jernigan; Zhijun Wu (J. Bioinform. Comput. Biol., 2008)

Refinement of under-determined loops of Human Prion Protein by database-derived distance constraints. - Feng Cui; Kriti Mukhopadhyay; Won-Bin Young; Robert L. Jernigan; Zhijun Wu (Int. J. Data Min. Bioinform., 2009)

PRTAD: A database for protein residue torsion angle distributions. - Xiaoyong Sun; Di Wu; Robert L. Jernigan; Zhijun Wu (Int. J. Data Min. Bioinform., 2009)

Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos. - Ataur R. Katebi; Pawel Gniewek; Michael T. Zimmermann; Saras Saraswathi; Zhenming Gong; Christopher K. Tuggle; Andrzej Kloczkowski; Robert L. Jernigan (BCB, 2010)

Immunoglobulin functional motions and their effects on the complementarity determining regions. - Michael T. Zimmermann; Aris Skliros; Saras Saraswathi; Andrzej Kloczkowski; Robert L. Jernigan (BCB, 2010)

Protein Secondary Structure Prediction using Knowledge-based Potentials. - Saras Saraswathi; Robert L. Jernigan; Andrzej Kloczkowski; Andrzej Kolinski (IJCCI (ICFC-ICNC), 2010)

An Extreme Learning Machine Classifier for Prediction of Relative Solvent Accessibility in Proteins. - Saras Saraswathi; Andrzej Kloczkowski; Robert L. Jernigan (IJCCI (ICFC-ICNC), 2010)

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. - Yaping Feng; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2010)

Particle Swarm Optimization: A Powerful Family of Stochastic Optimizers. Analysis, Design and Application to Inverse Modelling. - Juan Luis Fernández Martínez; Esperanza García Gonzalo; Saras Saraswathi; Robert L. Jernigan; Andrzej Kloczkowski (ICSI (1), 2011)

MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles. - Michael T. Zimmermann; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2011)

Analysis of protein dynamics using local-DME calculations. - Di Wu; Stephen Smith; Hannah Mahan; Robert L. Jernigan; Zhijun Wu (Int. J. Bioinform. Res. Appl., 2011)

Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein. - Michael T. Zimmermann; Robert L. Jernigan (Entropy, 2012)

P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics. - Yuanyuan Huang 004; Steve Bonett; Andrzej Kloczkowski; Robert L. Jernigan; Zhijun Wu (J. Bioinform. Comput. Biol., 2012)

A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly. - Brittany Burton; Michael T. Zimmermann; Robert L. Jernigan; Yongmei Wang (PLoS Comput. Biol., 2012)

An analysis of conformational changes upon RNA-protein binding. - Kannan Sankar; Rasna R. Walia; Carla M. Mann; Robert L. Jernigan; Vasant G. Honavar; Drena Dobbs (BCB, 2014)

PRESS-PLOT: An Online Server for Protein Structural Analysis and Evaluation with Residue-level Virtual Angle Correlation Plots. - Yuanyuan Huang 004; Kejue Jia; Robert L. Jernigan; Zhijun Wu (ISBRA, 2015)

Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models. - Sumudu P. Leelananda; Robert L. Jernigan; Andrzej Kloczkowski (RECOMB, 2015)

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. - Hyuntae Na; Robert L. Jernigan; Guang Song (PLoS Comput. Biol., 2015)

Session Introduction. - Drena Dobbs; Steven E. Brenner; Vasant G. Honavar; Robert L. Jernigan; Alain Laederach; Quaid Morris (PSB, 2016)

Fold-specific sequence scoring improves protein sequence matching. - Sumudu P. Leelananda; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2016)

Predicting Designability of Small Proteins from Graph Features of Contact Maps. - Sumudu P. Leelananda; Robert L. Jernigan; Andrzej Kloczkowski (J. Comput. Biol., 2016)

Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases. - Nikita Chopra; Thomas E. Wales; Raji E. Joseph; Scott E. Boyken; John R. Engen; Robert L. Jernigan; Amy H. Andreotti (PLoS Comput. Biol., 2016)

Characteristics of Protein Fold Space Exhibits Close Dependence on Domain Usage. - Michael T. Zimmermann; Fadi Towfic; Robert L. Jernigan; Andrzej Kloczkowski (IWBBIO (1), 2019)

Entropy, Fluctuations, and Disordered Proteins. - Eshel Faraggi; A. Keith Dunker; Robert L. Jernigan; Andrzej Kloczkowski (Entropy, 2019)

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. - Eshel Faraggi; Robert L. Jernigan; Andrzej Kloczkowski (Artificial Neural Networks, 3rd Edition, 2021)

Simulated Drug Efflux for the AbgT Family of Membrane Transporters. - Sayane Shome; Kannan Sankar; Robert L. Jernigan (J. Chem. Inf. Model., 2021)

Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier. - Ambuj Kumar; Pranav M. Khade; Karin S. Dorman; Robert L. Jernigan (Bioinform., 2022)

Predicting allosteric pockets in protein biological assemblages. - Ambuj Kumar; Burak T. Kaynak; Karin S. Dorman; Pemra Doruker; Robert L. Jernigan (Bioinform., 2023)

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions. - Kejue Jia; Mesih Kilinc; Robert L. Jernigan (Frontiers Bioinform., 2023)

Machine Learning-Based Tool for Efficient Discrimination Between Deleterious and Neutral Missense Mutations. - Eshel Faraggi; Robert L. Jernigan; Andrzej Kloczkowski (ICAISC (3), 2024)