Selected
Publications (out of 190 papers)
Myron P, Sen TZ , Jernigan RL and Kloczkowski A. Generation and enumeration of compact conformations on the 2D triangular and 3D fcc lattices. Submitted.
Flatow DF, Jernigan RL. Approximating Protein Volumes and Surfaces. Submitted.
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”, Ed. G Voth, Taylor and Francis Group, LLC, in press.
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, in press.
Yan C, Wu F, Jernigan RL, Dobbs D, Honavar V Characterization of Protein-Protein Interfaces. Protein J, in press
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
Yang L, Song G, Jernigan RL How well can we understand large-scale protein motions using elastic normal modes? Biophys J, in press.
Sulkowska JI, Kloczkowski A, Sen TZ, Cieplak M and Jernigan RL. Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins, in press.
Wu D, Jernigan R and Wu Z. Refinement of NMR-determined protein structures with database derived mean-force potentials. Proteins, in press.
Song G and Jernigan RL. vGNM: a Better Model for Understanding the Dynamics of Proteins in Crystals. J Mol Biol 2007 369:880-893.
Wu D, Cui F, Jernigan R, Wu, ZJ. Database for protein inter-atomic distance distributions. Nucl. Acids Res. 2007;35:D202-D207.
Peto M, Kloczkowski A, and Jernigan, RL. Shape-dependent designability studies of lattice proteins. J. Phys.: Cond. Matter , in press.
Pokarowski P, Kloczkowski A, Nowakowski S, Pokarowska M, Jernigan RL and Kolinski A.Ideal Amino Acid Exchange Forms for Approximating Substitution Matrices. Proteins, 2005 Apr 1;59(1):49-57.
Terribilini M, Lee JH, Yan C, Jernigan RL, Carpenter S, Honavar V, Dobbs D.. Identifying interaction sites in "recalcitrant" proteins: predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data. Pac. Symp. Biocomp. 2006;415-26.
TZ Sen, H Cheng, A Kloczkowski, RL Jernigan. A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining. Protein Sci., 2006; Sep 25; [Epub ahead of print]
C Yan, M Terribilini, F Wu, RL Jernigan, D Dobbs, V Honavar. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006;7:262.
M
Terribilini, JH Lee, C Yan, S Carpenter, R Jernigan, V Honavar, D Dobbs. Identifying interaction sites in
"recalcitrant" proteins: Predicted protein and RNA binding sites in Rev
proteins of HIV and EIAV agree with experimental data. Pac Symp Biocomput (PSB 06). Singapore: World Scientific Press. pp. 415-426.
O
Kurkcuoglu, RL Jernigan, P Doruker. Collective dynamics of large proteins
from mixed coarse-grained elastic network model. QSAR Comb Sci 2005
24:443-448.
Y
Wang, RL Jernigan. Comparison of tRNA Motions in the Free and Ribosomal
Bound Structures. Biophys J 2005 89:3399-3409.
TZ Sen, RL
Jernigan. Optimizing cutoff distances
and spring constants for the Gaussian Network Model of ATP-binding proteins, in
“Normal Mode Analysis: Theory and Applications to Biological and Chemical
Systems,” Eds. I. Bahar and Q. Cui, CRC Press in press.
TZ
Sen, RL Jernigan, J Garnier, A Kloczkowski. GOR V server for protein
Secondary dtructure prediction. Bioinformatics 2005 21:2787-2788.
H
Cheng, TZ Sen, A Kloczkowski, D Margaritis, RL Jernigan. Prediction of
protein secondary structure by mining structural fragment database. Polymer
2005 46:4314-4321.
A
Yan, RL Jernigan. How do sidechains orient globally in protein structures?
Proteins 2005 61:513-511.
H
Liao, W Yeh, D Chiang, RL Jernigan, B Lustig. Protein sequence entropy is
closely related to packing density and hydrophobicity. Prot Eng Des Select 2005
18:59-64.
P
Pokarowski, A Kloczkowski, RL Jernigan, NS Kothari, M Pokarowska, A Kolinski.
Inferring ideal amino acid interaction forms from statistical protein contact
potentials. Proteins: Struct Funct Bioinf 2005 59:49-57.
MK
Kim, RL Jernigan, GS Chirikjian. Rigid-cluster models of conformational
transitions in macromolecular machines and assemblies. Biophys J 2005
89:43-55.
A
Kloczkowski, TZ Sen, RL Jernigan. Promiscuous vs. native protein function.
Insights from studying collective motions in proteins by elastic network
models. J Biomol Struct Dyn 2005 22:621-624.
S
Miyazawa, RL Jernigan. How effective for fold recognition is a potential of
mean force that includes relative orientations between contacting residues in
proteins? J Chem Phys 2005 122:24901 1-18.
TZ
Sen, A Kloczkowski, RL Jernigan, C Yan, V Honavar, KM Ho, CZ Wang, Y Ihm, H Cao, X Gu, D Dobbs. Predicting binding sites of hydrolase-inhibitor
complexes by combining several methods.
BMC Bioinformatics 2004 5:205.
S
Kundu, RL Jernigan. Molecular Mechanism of Domain Swapping in Proteins:
An Analysis
of Slower Motions. Biophys J 2004
86:3846-3854.
Y
Wang, AJ Rader, I Bahar, RL Jernigan. Global Ribosome Motions Revealed with
Elastic Network Model. J Struct Biol 2004 147:302-14.
MY
Tolstorukov, RL Jernigan, VB Zhurkin. Protein-DNA hydrophobic recognition
in the minor groove is facilitated by sugar switching. J Mol Biol 2004 337:65-76.
AK
Shchyolkina, DN Kaluzhny, OF Borisova, ME Hawkins, RL Jernigan, TM Jovin, DJ
Arndt-Jovin, VB Zhurkin, Formation of an intramolecular triple-stranded DNA
structure monitored by fluorescence of 2-aminopurine or
6-methylisoxanthopterin. Nucl Acids
Res 2004 32:432-440.
A Kloczkowski,
RL Jernigan. Introduction to “Protein Conformational
Computations” - a special issue of Polymer.
2004 45:507.
O Kurkcuoglu, RL
Jernigan, P Doruker. Mixed levels of coarse-graining of large proteins
using elastic network model succeeds in extracting the slowest motions. Polymer 2004 45:649-657.
A Kloczkowski, TZ
Sen, RL Jernigan. The Transfer Matrix Method for Lattice Proteins –
An Application with Cooperative Interactions. Polymer 2004 45:707-716.
I
Navizet, RL Jernigan. Myosin flexibility: Structural domains and collective
vibrations. Proteins 2004
54:384-393.
P
Doruker, RL Jernigan. Functional motions can be extracted from on-lattice
construction of protein structures. Proteins
2003 53:174-181.
S
Miyazawa, RL Jernigan. Long- and short-range interactions in native protein
structures are consistent/minimally frustrated in sequence space. Proteins 2003 50:35-43.
MK
Kim, RL Jernigan, GS Chirikjian. An elastic network model of HK97 capsid
maturation. J Struct Biol 2003 143:107-117
Z Bagci, RL Jernigan,
I Bahar. Residue coordination in proteins conforms to the closest packing of
spheres. Polymer 2002 43:451-459.
P Doruker, RL
Jernigan, I Navizet, R Hernandez. Important fluctuation dynamics of large
protein structures are preserved upon renormalization. Int J Quantum Chem 2002
90:822-837.
O
Keskin, I Bahar. D Flatow, DG Covell, RL Jernigan. Molecular mechanisms of
chaperonin GroEL-GroES function. Biochemistry. 2002 41:491-501.
AR
Atilgan, SR Durell, RL Jernigan, MC Demirel, O Keskin, I Bahar. Anisotropy
of fluctuation dynamics of proteins with an elastic network model. Biophys J
2001 80:505-515.
O
Keskin, I Bahar, RL Jernigan, JA Beutler, RH Shoemaker, EA Sausville, DG
Covell. Characterization of Anticancer Agents by Their Growth Inhibitory
Activity and Relationships to Mechanism of Action and Structure. Anti-Cancer
Drug Design 2000 15:79-98.
O
Keskin, RL Jernigan, I Bahar. Proteins with Similar Architecture Exhibit
Similar Large-scale Dynamic Behavior. Biophys J 2000 78:2093-2106.
I
Bahar, B Erman, RL Jernigan, DG Covell. Collective motions in HIV-1 Reverse
Transcriptase: Examination of flexibility and enzyme function. J Mol Biol 1999
285:1023-1037.
I
Bahar, RL Jernigan. Vibrational dynamics of transfer RNAs: Comparison of
the free and synthetase-bound forms. J Mol Biol 1998 281 871-884.
I
Bahar, RL Jernigan. Inter-residue potentials in globular proteins and the
dominance of highly specific hydrophilic interactions at close separation. J
Mol Biol 1997 266:195-214.
S
Miyazawa, RL Jernigan. Residue-Residue Potentials with a Favorable Contact
Pair Term and an Unfavorable High Packing Density Term for Simulation and
Threading. J Mol Biol 1996 256:623-644.
S
Miyazawa, RL Jernigan. Protein stability changes for single substitution
mutants and the extent of local compactness in the denatured state. Prot Eng
1994 7:1209-1220.
L
Young, D Covell, RL Jernigan. A Role for surface hydrophobicity in
protein-protein recognition. Prot Sci 1994 3:717-729.
VB
Zhurkin, G Raghunathan, NB Ulyanov, RD Camerini-Otero, RL Jernigan. A
parallel DNA triplex as a model for the intermediate in homologous
recombination. J Mol Biol 1994 239:181-200.
S
Miyazawa, RL Jernigan. A new substitution matrix for protein sequence
searches based on contact frequencies in protein structures. Prot Eng 1993
6:267-278.
DG
Covell, D.G., RL Jernigan. Conformations of folded proteins in restricted
spaces. Biochemistry 1990 29: 3287-3294.
A
Sarai, J Mazur, R Nussinov, RL Jernigan. Sequence dependence of DNA
conformational flexibility. Biochemistry 1989 28:7842-7849.
A
Sarai, J Mazur, R Nussinov, RL Jernigan. Origin of DNA helical structure
and its sequence dependence. Biochemistry 1988 27:8498-8502.
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