Professor
Director, Baker Center
for Bioinformatics and Biological Statistics
Theoretical studies on the structures of proteins, nucleic acids, and
small molecules
Applications of theoretical studies to develop molecular models and
to select new drugs
Selected Publications
Wu D, Cui F, Jernigan R, Wu, ZJ PIDD: Database for protein inter-atomic distance distributions. Nucl Acids Res 2007;35:D202-D207.
Pokarowski P, Kloczkowski A, Nowakowski S, Pokarowska M, Jernigan RL, Kolinski A Ideal Amino Acid Exchange Forms for Approximating Substitution Matrices. Proteins, 2007, 69:379-393.
Peto M, Kloczkowski A, Jernigan RL Shape-dependent designability studies of lattice proteins. J Phys: Condensed Matter 2007; 19:285220-285230.
Song G, Jernigan RL vGNM: a Better Model for Understanding the Dynamics of Proteins in Crystals. J Mol Biol 2007; 369:880-893.
Wu D, Jernigan R, Wu Z Refinement of NMR-determined protein structures with database derived mean-force potentials. Proteins 2007; 68,:232-242.
Yang L, Song G, Jernigan RL How well can we understand large-scale protein motions using elastic normal modes? Biophys J 2007; 93:920-929.
Feng Y, Kloczkowski A, Jernigan RL Four-body contact potentials derived from two protein databases to discriminate native structures from decoys. Proteins 2007; 68:57-66.
Peto M, Sen TZ , Jernigan RL, Kloczkowski A Generation and enumeration of compact conformations on the 2-dimensional triangular and 3-dimensional fcc lattices. J Chem Phys 2007; 127:044101.
Terribilini M, Sander JD, Lee J-H, Zaback P, Jernigan RL, Honavar V, Dobbs D RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucl Acids Res 2007; 35:W578-584.
Yan A, Kloczkowski A, Hofmann H, Jernigan RL Prediction of side chain orientations in proteins by statistical machine learning methods. J Biomol Struct Dyn 2007; 25:275-288.
Cheng H, Sen TZ, Jernigan RL, Kloczkowski A Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). Bioinformatics 2007; 23:2628-30.
Sułkowska JI, Kloczkowski A, Sen TZ, Cieplak M, Jernigan RL Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins 2007, 71:45-60.
Yan C, Wu F, Jernigan RL, Dobbs D, Honavar V Characterization of Protein-Protein Interfaces. Protein J 2008 27:59-70.
Yang L, Song G, Carriquiry A, Jernigan RL Close Correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure 2008 16:321-330.
Jernigan RL, Yang L, Song G, Doruker P Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics. in “Coarse-Graining of Condensed Phase and Biomolecular Systems” G Voth (Ed) Taylor and Francis Group, LLC, 2008, in press.
Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA. Biophys J 2008;94:2482-2491.
Schuyler, AD, Jernigan RL, Qasba PK, Ramakrishnan B, Chirikjian GS Iterative cluster-NMA (icNMA): A tool for generating conformational transitions in proteins Proteins 2008, in press.
Kloczkowski, A, Jernigan, RL Book review of molecular modeling of proteins. Methods in molecular biology, 443. J Am Chem Soc 2008;130:12548.
Feng, Y, Jernigan, RL, Kloczkowski, A. Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron. Proteins 2008 in press.
Cui, F, Jernigan, R, Wu, Z Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement. J Bioinform Comput Biol 2008;6:283-300.
Yan A, Wang Y, Kloczkowski A, Jernigan RL Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome J. Chem. Thy. Comput.,2008 in press.
