Robert L. Jernigan - Publications

Iowa State University, Ames, IA, United States 

173 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Shome S, Sankar K, Jernigan RL. Simulated Drug Efflux for the AbgT Family of Membrane Transporters. Journal of Chemical Information and Modeling. 61: 5673-5681. PMID 34714659 DOI: 10.1021/acs.jcim.1c00516  1
2021 Khade PM, Scaramozzino D, Kumar A, Lacidogna G, Carpinteri A, Jernigan RL. hdANM: a new comprehensive dynamics model for protein hinges. Biophysical Journal. PMID 34687719 DOI: 10.1016/j.bpj.2021.10.017  1
2021 Kumar A, Jernigan RL. Ligand Binding Introduces Significant Allosteric Shifts in the Locations of Protein Fluctuations. Frontiers in Molecular Biosciences. 8: 733148. PMID 34540902 DOI: 10.3389/fmolb.2021.733148  1
2021 Ehrlich JJ, Weerts RM, Shome S, Culbertson AT, Honzatko RB, Jernigan RL, Zabotina OA. Xyloglucan Xylosyltransferase 1 Displays Promiscuity Toward Donor Substrates During In vitro Reactions. Plant & Cell Physiology. PMID 34265062 DOI: 10.1093/pcp/pcab114  1
2021 Jia K, Jernigan RL, Carver RJ. New Amino Acid Substitution Matrix Brings Sequence Alignments into Agreement with Structure Matches. Proteins. PMID 33469973 DOI: 10.1002/prot.26050  1
2021 Faraggi E, Jernigan RL, Kloczkowski A. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Methods in Molecular Biology (Clifton, N.J.). 2190: 307-316. PMID 32804373 DOI: 10.1007/978-1-0716-0826-5_15  1
2020 Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Frontiers in Molecular Biosciences. 7: 607323. PMID 33614705 DOI: 10.3389/fmolb.2020.607323  1
2020 Scaramozzino D, Khade PM, Jernigan RL, Lacidogna G, Carpinteri A. Structural Compliance - A New Metric for Protein Flexibility. Proteins. PMID 32548853 DOI: 10.1002/prot.25968  1
2020 Kono A, Chou TH, Radhakrishnan A, Bolla JR, Sankar K, Shome S, Su CC, Jernigan RL, Robinson CV, Yu EW, Spalding MH. Structure and Function of LCI1: A plasma membrane CO channel in the Chlamydomonas CO concentrating mechanism. The Plant Journal : For Cell and Molecular Biology. PMID 32168387 DOI: 10.1111/Tpj.14745  1
2019 Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel, Switzerland). 21. PMID 32336912 DOI: 10.3390/E21080764  1
2019 Khade PM, Kumar A, Jernigan RL. Characterizing and Predicting Protein Hinges for Mechanistic Insight. Journal of Molecular Biology. PMID 31786268 DOI: 10.1016/J.Jmb.2019.11.018  1
2019 Jia M, Mishra SK, Tufts S, Jernigan RL, Peters RJ. Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases. Metabolic Engineering. PMID 31220664 DOI: 10.1016/J.Ymben.2019.06.008  1
2019 Mishra SK, Kandoi G, Jernigan RL. Coupling Dynamics and Evolutionary Information with Structure to Identify Protein Regulatory and Functional Binding Sites. Proteins. PMID 31141211 DOI: 10.1002/prot.25749  1
2018 Mishra SK, Jernigan RL. Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics. Plos One. 13: e0199225. PMID 29924847 DOI: 10.1371/journal.pone.0199225  1
2018 Sankar K, Mishra SK, Jernigan RL. Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models. The Journal of Physical Chemistry. B. PMID 29376347 DOI: 10.1021/acs.jpcb.7b11668  1
2018 Testroet ED, Shome S, Reecy JM, Jernigan RL, Zhu M, Du M, Clark S, Beitz DC. Profiling of the Exosomal Cargo of Bovine Milk Reveals the Presence of Immune- and Growth-modulatory Non-coding RNAs (ncRNA) Animal Industry Report. 664: 33. DOI: 10.31274/Ans_Air-180814-330  0.24
2017 Liu J, Sankar K, Wang Y, Jia K, Jernigan RL. Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change. Biophysical Journal. 112: 1561-1570. PMID 28445748 DOI: 10.1016/J.Bpj.2017.03.004  1
2017 Mishra SK, Sankar K, Jernigan RL. Altered Dynamics upon Oligomerization Corresponds to Key Functional Sites. Proteins. PMID 28383162 DOI: 10.1002/prot.25302  1
2017 Sankar K, Jia K, Jernigan RL. Knowledge-based entropies improve the identification of native protein structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28265078 DOI: 10.1073/pnas.1613331114  1
2017 Kandoi G, Leelananda SP, Jernigan RL, Sen TZ. Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information. Methods in Molecular Biology (Clifton, N.J.). 1484: 35-44. PMID 27787818 DOI: 10.1007/978-1-4939-6406-2_4  1
2016 Manibog K, Sankar K, Kim SA, Zhang Y, Jernigan RL, Sivasankar S. Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 27621473 DOI: 10.1073/Pnas.1604012113  1
2016 Leelananda SP, Kloczkowski A, Jernigan RL. Fold-specific sequence scoring improves protein sequence matching. Bmc Bioinformatics. 17: 328. PMID 27578239 DOI: 10.1186/S12859-016-1198-Z  1
2016 Leelananda SP, Jernigan RL, Kloczkowski A. Predicting Designability of Small Proteins from Graph Features of Contact Maps. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 23: 400-11. PMID 27159634 DOI: 10.1089/Cmb.2015.0209  1
2016 Chopra N, Wales TE, Joseph RE, Boyken SE, Engen JR, Jernigan RL, Andreotti AH. Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases. Plos Computational Biology. 12: e1004826. PMID 27010561 DOI: 10.1371/Journal.Pcbi.1004826  1
2016 Zimmermann MT, Jia K, Jernigan RL. Ribosome Mechanics Informs about Mechanism. Journal of Molecular Biology. 428: 802-10. PMID 26687034 DOI: 10.1016/J.Jmb.2015.12.003  1
2016 Rashin AA, Jernigan RL. Clusters of Structurally Similar MHC I HLA-A2 Molecules, Found with a New Method, Suggest Mechanisms of T-Cell Receptor Avidity. Biochemistry. 55: 167-85. PMID 26600404 DOI: 10.1021/Acs.Biochem.5B01077  1
2015 Sankar K, Liu J, Wang Y, Jernigan RL. Distributions of experimental protein structures on coarse-grained free energy landscapes. The Journal of Chemical Physics. 143: 243153. PMID 26723638 DOI: 10.1063/1.4937940  1
2015 Na H, Jernigan RL, Song G. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. Plos Computational Biology. 11: e1004542. PMID 26473491 DOI: 10.1371/Journal.Pcbi.1004542  1
2015 Jiang F, An C, Bao Y, Zhao X, Jernigan RL, Lithio A, Nettleton D, Li L, Wurtele ES, Nolan LK, Lu C, Li G. ArcA Controls Metabolism, Chemotaxis and Motility Contributing to the Pathogenicity of Avian Pathogenic E. coli. Infection and Immunity. PMID 26099584 DOI: 10.1128/Iai.00312-15  1
2015 Katebi AR, Jernigan RL. Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics. Biochemistry. 54: 3543-54. PMID 25982518 DOI: 10.1021/Acs.Biochem.5B00042  1
2015 Katebi AR, Sankar K, Jia K, Jernigan RL. The use of experimental structures to model protein dynamics. Methods in Molecular Biology (Clifton, N.J.). 1215: 213-36. PMID 25330965 DOI: 10.1007/978-1-4939-1465-4_10  1
2015 Zimmermann MT, Jia K, Jernigan RL. Ribosome Mechanics Informs about Mechanism Journal of Molecular Biology. DOI: 10.1016/j.jmb.2015.12.003  1
2014 Boyken SE, Chopra N, Xie Q, Joseph RE, Wales TE, Fulton DB, Engen JR, Jernigan RL, Andreotti AH. A conserved isoleucine maintains the inactive state of Bruton's tyrosine kinase. Journal of Molecular Biology. 426: 3656-69. PMID 25193673 DOI: 10.1016/J.Jmb.2014.08.018  1
2014 Zimmermann MT, Jernigan RL. Elastic network models capture the motions apparent within ensembles of RNA structures. Rna (New York, N.Y.). 20: 792-804. PMID 24759093 DOI: 10.1261/Rna.041269.113  1
2014 Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL. Factors correlating with significant differences between X-ray structures of myoglobin. Acta Crystallographica. Section D, Biological Crystallography. 70: 481-91. PMID 24531482 DOI: 10.1107/S1399004713028812  1
2014 Katebi AR, Jernigan RL. The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality. Protein Science : a Publication of the Protein Society. 23: 213-28. PMID 24318986 DOI: 10.1002/Pro.2407  1
2014 Afonin KA, Kasprzak W, Bindewald E, Puppala PS, Diehl AR, Hall KT, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA. Computational and experimental characterization of RNA cubic nanoscaffolds. Methods (San Diego, Calif.). 67: 256-65. PMID 24189588 DOI: 10.1016/J.Ymeth.2013.10.013  1
2014 Flatow D, Leelananda SP, Skliros A, Kloczkowski A, Jernigan RL. Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures. Current Pharmaceutical Design. 20: 1208-22. PMID 23713774 DOI: 10.2174/13816128113199990067  1
2014 Sankar K, Jernigan RL, Walia RR, Honavar VG, Mann CM, Dobbs D. An analysis of conformational changes upon RNA-Protein binding Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 592-593. DOI: 10.1145/2649387.2660790  1
2013 Park JK, Jernigan R, Wu Z. Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations. Bulletin of Mathematical Biology. 75: 124-60. PMID 23296997 DOI: 10.1007/S11538-012-9797-Y  1
2013 Gu Y, Sun W, Wang G, Zimmermann MT, Jernigan RL, Fang N. Revealing rotational modes of functionalized gold nanorods on live cell membranes. Small (Weinheim An Der Bergstrasse, Germany). 9: 785-92. PMID 23124917 DOI: 10.1002/Smll.201201808  1
2012 Huang Y, Bonett S, Kloczkowski A, Jernigan R, Wu Z. P.R.E.S.S.--an R-package for exploring residual-level protein structural statistics. Journal of Bioinformatics and Computational Biology. 10: 1242007. PMID 22809383 DOI: 10.1142/S0219720012420073  1
2012 Burton B, Zimmermann MT, Jernigan RL, Wang Y. A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. Plos Computational Biology. 8: e1002530. PMID 22654657 DOI: 10.1371/Journal.Pcbi.1002530  1
2012 Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. Elastic network normal modes provide a basis for protein structure refinement. The Journal of Chemical Physics. 136: 195101. PMID 22612113 DOI: 10.1063/1.4710986  1
2012 Zimmermann MT, Leelananda SP, Kloczkowski A, Jernigan RL. Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses. The Journal of Physical Chemistry. B. 116: 6725-31. PMID 22490366 DOI: 10.1021/Jp2120143  1
2012 Skliros A, Zimmermann MT, Chakraborty D, Saraswathi S, Katebi AR, Leelananda SP, Kloczkowski A, Jernigan RL. The importance of slow motions for protein functional loops. Physical Biology. 9: 014001. PMID 22314977 DOI: 10.1088/1478-3975/9/1/014001  1
2012 Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. How noise in force fields can affect the structural refinement of protein models? Proteins. 80: 335-41. PMID 22223184 DOI: 10.1002/Prot.23240  1
2011 Zimmermann MT, Skliros A, Kloczkowski A, Jernigan RL. Immunoglobulin Structure Exhibits Control over CDR Motion. Immunome Research. 7. PMID 25191522 DOI: 10.4172/1745-7580.1000047  1
2011 Zimmermann MT, Kloczkowski A, Jernigan RL. MAVENs: motion analysis and visualization of elastic networks and structural ensembles. Bmc Bioinformatics. 12: 264. PMID 21711533 DOI: 10.1186/1471-2105-12-264  1
2011 Leelananda SP, Towfic F, Jernigan RL, Kloczkowski A. Exploration of the relationship between topology and designability of conformations. The Journal of Chemical Physics. 134: 235101. PMID 21702580 DOI: 10.1063/1.3596947  1
2011 Zimmermann MT, Leelananda SP, Gniewek P, Feng Y, Jernigan RL, Kloczkowski A. Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. Journal of Structural and Functional Genomics. 12: 137-47. PMID 21674234 DOI: 10.1007/S10969-011-9113-3  1
2011 Steczkiewicz K, Zimmermann MT, Kurcinski M, Lewis BA, Dobbs D, Kloczkowski A, Jernigan RL, Kolinski A, Ginalski K. Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step. Proceedings of the National Academy of Sciences of the United States of America. 108: 9443-8. PMID 21606328 DOI: 10.1073/Pnas.1015399108  1
2011 Wu D, Smith S, Mahan H, Jernigan RL. Analysis of protein dynamics using local-DME calculations. International Journal of Bioinformatics Research and Applications. 7: 146-61. PMID 21576073 DOI: 10.1504/Ijbra.2011.040093  1
2011 Gniewek P, Leelananda SP, Kolinski A, Jernigan RL, Kloczkowski A. Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins. 79: 1923-9. PMID 21560165 DOI: 10.1002/Prot.23015  1
2011 Huang Y, Bonett S, Kloczkowski A, Jernigan R, Wu Z. Statistical measures on residue-level protein structural properties. Journal of Structural and Functional Genomics. 12: 119-36. PMID 21452025 DOI: 10.7490/F1000Research.1273.1  1
2011 Su CC, Long F, Zimmermann MT, Rajashankar KR, Jernigan RL, Yu EW. Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli. Nature. 470: 558-62. PMID 21350490 DOI: 10.1038/Nature09743  1
2010 Skliros A, Jernigan RL, Kloczkowski A. Models to Approximate the Motions of Protein Loops. Journal of Chemical Theory and Computation. 6: 3249-3258. PMID 21031141 DOI: 10.1021/Ct1001413  1
2010 Long F, Su CC, Zimmermann MT, Boyken SE, Rajashankar KR, Jernigan RL, Yu EW. Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport. Nature. 467: 484-8. PMID 20865003 DOI: 10.1038/Nature09395  1
2010 Katebi AR, Kloczkowski A, Jernigan RL. Structural interpretation of protein-protein interaction network. Bmc Structural Biology. 10: S4. PMID 20487511 DOI: 10.1186/1472-6807-10-S1-S4  1
2010 Rashin AA, Rashin AH, Jernigan RL. Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability. Biochemistry. 49: 5683-704. PMID 20469886 DOI: 10.1021/Bi100110X  1
2010 Feng Y, Kloczkowski A, Jernigan RL. Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. Bmc Bioinformatics. 11: 92. PMID 20163737 DOI: 10.1186/1471-2105-11-92  1
2010 Zimmermann MT, Skliros A, Saraswathi S, Kloczkowski A, Jernigan RL. Immunoglobulin functional motions and their effects on the complementarity determining regions 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 621-626. DOI: 10.1145/1854776.1854892  1
2010 Katebi AR, Gniewek P, Zimmermann M, Saraswathi S, Gong Z, Tuggle CK, Kloczkowski A, Jernigan RL. Immunological implications of a structural analysis of two different porcine IL 1β proteins expressed in macrophages and embryos 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 653-655. DOI: 10.1145/1854776.1854890  1
2009 Sun X, Di W, Jernigan R, Wu Z. PRTAD: a database for protein residue torsion angle distributions. International Journal of Data Mining and Bioinformatics. 3: 469-82. PMID 20052908 DOI: 10.1504/IJDMB.2009.029207  1
2009 Cui F, Mukhopadhyay K, Young WB, Jernigan RL, Wu Z. Refinement of under-determined loops of Human Prion Protein by database-derived distance constraints. International Journal of Data Mining and Bioinformatics. 3: 454-68. PMID 20052907  1
2009 Zimmermann M, Towfic F, Jernigan RL, Kloczkowski A. Short paths in protein structure space originate in graph structure. Proceedings of the National Academy of Sciences of the United States of America. 106: E137; author reply E. PMID 20018710 DOI: 10.1073/Pnas.0912339106  1
2009 Rashin AA, Rashin AH, Jernigan RL. Protein flexibility: coordinate uncertainties and interpretation of structural differences. Acta Crystallographica. Section D, Biological Crystallography. 65: 1140-61. PMID 19923711 DOI: 10.1107/S090744490903145X  1
2009 Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophysical Journal. 97: 1178-87. PMID 19686666 DOI: 10.1016/J.Bpj.2009.06.009  1
2009 Yang L, Song G, Jernigan RL. Protein elastic network models and the ranges of cooperativity. Proceedings of the National Academy of Sciences of the United States of America. 106: 12347-52. PMID 19617554 DOI: 10.1073/Pnas.0902159106  1
2009 Feng Y, Yang L, Kloczkowski A, Jernigan RL. The energy profiles of atomic conformational transition intermediates of adenylate kinase. Proteins. 77: 551-8. PMID 19507242 DOI: 10.1002/Prot.22467  1
2009 Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, Kolinski A, Pokarowski P. Distance matrix-based approach to protein structure prediction. Journal of Structural and Functional Genomics. 10: 67-81. PMID 19224393 DOI: 10.1007/S10969-009-9062-2  1
2009 Yang L, Song G, Jernigan RL. Comparisons of experimental and computed protein anisotropic temperature factors. Proteins. 76: 164-75. PMID 19127591 DOI: 10.1002/Prot.22328  1
2009 Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins. 75: 837-45. PMID 19004020 DOI: 10.1002/Prot.22292  1
2009 Schuyler AD, Jernigan RL, Qasba PK, Ramakrishnan B, Chirikjian GS. Iterative cluster-NMA: A tool for generating conformational transitions in proteins. Proteins. 74: 760-76. PMID 18712827 DOI: 10.1002/Prot.22200  1
2008 Yan A, Wang Y, Kloczkowski A, Jernigan RL. Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome. Journal of Chemical Theory and Computation. 4: 1757-1767. PMID 19771145 DOI: 10.1021/Ct800223G  1
2008 Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Physical Biology. 5: 046005. PMID 19029596 DOI: 10.1088/1478-3975/5/4/046005  1
2008 Peto M, Kloczkowski A, Honavar V, Jernigan RL. Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. Bmc Bioinformatics. 9: 487. PMID 19014713 DOI: 10.1186/1471-2105-9-487  1
2008 Feng Y, Jernigan RL, Kloczkowski A. Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron. Proteins. 73: 730-41. PMID 18498111 DOI: 10.1002/Prot.22092  1
2008 Cui F, Jernigan R, Wu Z. Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement. Journal of Bioinformatics and Computational Biology. 6: 283-300. PMID 18464323 DOI: 10.1142/S0219720008003448  1
2008 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 (London, England : 1993). 16: 321-30. PMID 18275822 DOI: 10.1016/J.Str.2007.12.011  1
2008 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. Biophysical Journal. 94: 2482-91. PMID 18178655 DOI: 10.1529/Biophysj.107.116046  1
2008 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. 71: 45-60. PMID 17932935 DOI: 10.1002/Prot.21652  1
2008 Yan C, Wu F, Jernigan RL, Dobbs D, Honavar V. Characterization of protein-protein interfaces. The Protein Journal. 27: 59-70. PMID 17851740 DOI: 10.1007/S10930-007-9108-X  1
2007 Peto M, Kloczkowski A, Jernigan RL. Shape-dependent designability studies of lattice proteins. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 19: 285220-285230. PMID 18079979 DOI: 10.1088/0953-8984/19/28/285220  1
2007 Yan A, Kloczkowski A, Hofmann H, Jernigan RL. Prediction of side chain orientations in proteins by statistical machine learning methods. Journal of Biomolecular Structure & Dynamics. 25: 275-88. PMID 17937489 DOI: 10.1080/07391102.2007.10507176  1
2007 Peto M, Sen TZ, Jernigan RL, Kloczkowski A. Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices. The Journal of Chemical Physics. 127: 044101. PMID 17672675 DOI: 10.1063/1.2751169  1
2007 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 (Oxford, England). 23: 2628-30. PMID 17660202 DOI: 10.1093/Bioinformatics/Btm379  1
2007 Pokarowski P, Kloczkowski A, Nowakowski S, Pokarowska M, Jernigan RL, Kolinski A. Ideal amino acid exchange forms for approximating substitution matrices Proteins: Structure, Function and Genetics. 69: 379-393. PMID 17623859 DOI: 10.1002/Prot.21509  1
2007 Terribilini M, Sander JD, Lee JH, Zaback P, Jernigan RL, Honavar V, Dobbs D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Research. 35: W578-84. PMID 17483510 DOI: 10.1093/Nar/Gkm294  1
2007 Yang L, Song G, Jernigan RL. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophysical Journal. 93: 920-9. PMID 17483178 DOI: 10.1529/Biophysj.106.095927  1
2007 Song G, Jernigan RL. vGNM: a better model for understanding the dynamics of proteins in crystals. Journal of Molecular Biology. 369: 880-93. PMID 17451743 DOI: 10.1016/J.Jmb.2007.03.059  1
2007 Feng Y, Kloczkowski A, Jernigan RL. Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins. 68: 57-66. PMID 17393455 DOI: 10.1002/Prot.21362  1
2007 Wu D, Jernigan R, Wu Z. Refinement of NMR-determined protein structures with database derived mean-force potentials. Proteins. 68: 232-42. PMID 17387736 DOI: 10.1002/Prot.21358  1
2007 Wu D, Cui F, Jernigan R, Wu Z. PIDD: database for Protein Inter-atomic Distance Distributions. Nucleic Acids Research. 35: D202-7. PMID 17151078 DOI: 10.1093/Nar/Gkl802  1
2007 Jernigan RL, Kloczkowski A. Packing regularities in biological structures relate to their dynamics. Methods in Molecular Biology (Clifton, N.J.). 350: 251-76. PMID 16957327 DOI: 10.1385/1-59745-189-4:251  1
2006 Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL. The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. Journal of Chemical Theory and Computation. 2: 696-704. PMID 17710199 DOI: 10.1021/Ct600060D  1
2006 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. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 415-26. PMID 17094257  1
2006 Sen TZ, Cheng H, Kloczkowski A, Jernigan RL. A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining. Protein Science : a Publication of the Protein Society. 15: 2499-506. PMID 17001039 DOI: 10.1110/Ps.062125306  1
2006 Sen TZ, Kloczkowski A, Jernigan RL. A DNA-centric look at protein-DNA complexes. Structure (London, England : 1993). 14: 1341-2. PMID 16962964 DOI: 10.1016/J.Str.2006.08.003  1
2006 Sen TZ, Kloczkowski A, Jernigan RL. Functional clustering of yeast proteins from the protein-protein interaction network. Bmc Bioinformatics. 7: 355. PMID 16863590 DOI: 10.1186/1471-2105-7-355  1
2006 Terribilini M, Lee JH, Yan C, Jernigan RL, Honavar V, Dobbs D. Prediction of RNA binding sites in proteins from amino acid sequence. Rna (New York, N.Y.). 12: 1450-62. PMID 16790841 DOI: 10.1261/Rna.2197306  1
2006 Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence. Bmc Bioinformatics. 7: 262. PMID 16712732 DOI: 10.1186/1471-2105-7-262  1
2006 Song G, Jernigan RL. An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins. 63: 197-209. PMID 16447281 DOI: 10.1002/Prot.20836  1
2006 Kurkcuoglu O, Jernigan RL, Doruker P. Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry. 45: 1173-82. PMID 16430213 DOI: 10.1021/Bi0518085  1
2005 Cheng H, Sen TZ, Kloczkowski A, Margaritis D, Jernigan RL. Prediction of protein secondary structure by mining structural fragment database. Polymer. 46: 4314-4321. PMID 19081746 DOI: 10.1016/J.Polymer.2005.02.040  1
2005 Cui F, Jernigan R, Wu Z. Refinement of NMR-determined protein structures with database derived distance constraints. Journal of Bioinformatics and Computational Biology. 3: 1315-29. PMID 16374909 DOI: 10.1142/S0219720005001582  1
2005 Yan A, Jernigan RL. How do side chains orient globally in protein structures? Proteins. 61: 513-22. PMID 16152644 DOI: 10.1002/Prot.20638  1
2005 Wang Y, Jernigan RL. Comparison of tRNA motions in the free and ribosomal bound structures. Biophysical Journal. 89: 3399-409. PMID 16113113 DOI: 10.1529/Biophysj.105.064840  1
2005 Kim MK, Jernigan RL, Chirikjian GS. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. Biophysical Journal. 89: 43-55. PMID 15833998 DOI: 10.1529/Biophysj.104.044347  1
2005 Sen TZ, Jernigan RL, Garnier J, Kloczkowski A. GOR V server for protein secondary structure prediction. Bioinformatics (Oxford, England). 21: 2787-8. PMID 15797907 DOI: 10.1093/Bioinformatics/Bti408  1
2005 Liao H, Yeh W, Chiang D, Jernigan RL, Lustig B. Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Engineering, Design & Selection : Peds. 18: 59-64. PMID 15788422 DOI: 10.1093/protein/gzi009  1
2005 Pokarowski P, Kloczkowski A, Jernigan RL, Kothari NS, Pokarowska M, Kolinski A. Inferring ideal amino acid interaction forms from statistical protein contact potentials. Proteins. 59: 49-57. PMID 15688450 DOI: 10.1002/Prot.20380  1
2005 Miyazawa S, Jernigan RL. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? The Journal of Chemical Physics. 122: 024901. PMID 15638624 DOI: 10.1063/1.1824012  1
2004 Sen TZ, Kloczkowski A, Jernigan RL, Yan C, Honavar V, Ho KM, Wang CZ, Ihm Y, Cao H, Gu X, Dobbs D. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. Bmc Bioinformatics. 5: 205. PMID 15606919 DOI: 10.1186/1471-2105-5-205  1
2004 Wang Y, Rader AJ, Bahar I, Jernigan RL. Global ribosome motions revealed with elastic network model. Journal of Structural Biology. 147: 302-14. PMID 15450299 DOI: 10.1016/J.Jsb.2004.01.005  1
2004 Kundu S, Jernigan RL. Molecular mechanism of domain swapping in proteins: an analysis of slower motions. Biophysical Journal. 86: 3846-54. PMID 15189881 DOI: 10.1529/Biophysj.103.034736  0.01
2004 Tolstorukov MY, Jernigan RL, Zhurkin VB. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. Journal of Molecular Biology. 337: 65-76. PMID 15001352 DOI: 10.1016/J.Jmb.2004.01.011  1
2004 Navizet I, Lavery R, Jernigan RL. Myosin flexibility: structural domains and collective vibrations. Proteins. 54: 384-93. PMID 14747987 DOI: 10.1002/Prot.10476  1
2004 Shchyolkina AK, Kaluzhny DN, Borisova OF, Hawkins ME, Jernigan RL, Jovin TM, Arndt-Jovin DJ, Zhurkin VB. Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin. Nucleic Acids Research. 32: 432-40. PMID 14739235 DOI: 10.1093/Nar/Gkh158  1
2003 Doruker P, Jernigan RL. Functional motions can be extracted from on-lattice construction of protein structures. Proteins. 53: 174-81. PMID 14517969 DOI: 10.1002/Prot.10486  1
2003 Kim MK, Jernigan RL, Chirikjian GS. An elastic network model of HK97 capsid maturation. Journal of Structural Biology. 143: 107-17. PMID 12972347 DOI: 10.1016/S1047-8477(03)00126-6  1
2003 Bagci Z, Kloczkowski A, Jernigan RL, Bahar I. The origin and extent of coarse-grained regularities in protein internal packing. Proteins. 53: 56-67. PMID 12945049 DOI: 10.1002/Prot.10435  1
2003 Miyazawa S, Jernigan RL. Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space. Proteins. 50: 35-43. PMID 12471597 DOI: 10.1002/Prot.10242  1
2002 Kloczkowski A, Jernigan RL. Loop folds in proteins and evolutionary conservation of folding nuclei. Journal of Biomolecular Structure & Dynamics. 20: 323-5. PMID 12437369 DOI: 10.1080/07391102.2002.10506849  1
2002 Kim MK, Chirikjian GS, Jernigan RL. Elastic models of conformational transitions in macromolecules. Journal of Molecular Graphics & Modelling. 21: 151-60. PMID 12398345 DOI: 10.1016/S1093-3263(02)00143-2  1
2002 Kloczkowski A, Ting KL, Jernigan RL, Garnier J. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins. 49: 154-66. PMID 12210997 DOI: 10.1002/Prot.10181  1
2002 Kim MK, Jernigan RL, Chirikjian GS. Efficient generation of feasible pathways for protein conformational transitions. Biophysical Journal. 83: 1620-30. PMID 12202386 DOI: 10.1016/S0006-3495(02)73931-3  1
2002 Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophysical Journal. 83: 663-80. PMID 12124255 DOI: 10.1016/S0006-3495(02)75199-0  1
2002 Ting KL, Jernigan RL. Identifying a folding nucleus for the lysozyme/alpha-lactalbumin family from sequence conservation clusters. Journal of Molecular Evolution. 54: 425-36. PMID 11956682 DOI: 10.1007/s00239-001-0033-x  1
2002 Doruker P, Jernigan RL, Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. Journal of Computational Chemistry. 23: 119-27. PMID 11913377 DOI: 10.1002/Jcc.1160  1
2002 Mansfield ML, Covell DG, Jernigan RL. A new class of molecular shape descriptors. 1. Theory and properties. Journal of Chemical Information and Computer Sciences. 42: 259-73. PMID 11911695 DOI: 10.1021/Ci000100O  1
2002 Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41: 491-501. PMID 11781087 DOI: 10.1021/Bi011393X  0.36
2001 Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal. 80: 505-15. PMID 11159421 DOI: 10.1016/S0006-3495(01)76033-X  1
2000 Keskin O, Bahar I, Jernigan RL, Beutler JA, Shoemaker RH, Sausville EA, Covell DG. Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure. Anti-Cancer Drug Design. 15: 79-98. PMID 10901296 DOI: 10.5072/Zenodo.19292  1
2000 Keskin O, Jernigan RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophysical Journal. 78: 2093-106. PMID 10733987 DOI: 10.1016/S0006-3495(00)76756-7  0.36
1999 Bahar I, Jernigan RL. Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry. 38: 3478-90. PMID 10090734 DOI: 10.1021/Bi982697V  0.52
1999 Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell DG. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. Journal of Molecular Biology. 285: 1023-37. PMID 9887265 DOI: 10.1006/Jmbi.1998.2371  0.44
1999 Keskin O, Bahar I, Badretdinov AY, Ptitsyn OB, Jernigan RL. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Science : a Publication of the Protein Society. 7: 2578-86. PMID 9865952 DOI: 10.1002/Pro.5560071211  0.68
1999 Jernigan RL, Demirel MC, Bahar I. Relating Structure to Function Through the Dominant Slow Modes of Motion of DNA Topoisomerase II International Journal of Quantum Chemistry. 75: 301-312. DOI: 10.1002/(Sici)1097-461X(1999)75:3<301::Aid-Qua19>3.0.Co;2-0  1
1998 Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I. Identification of kinetically hot residues in proteins. Protein Science : a Publication of the Protein Society. 7: 2522-32. PMID 9865946 DOI: 10.1002/Pro.5560071205  1
1998 Lustig B, Bahar I, Jernigan RL. RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access. Nucleic Acids Research. 26: 5212-7. PMID 9801321 DOI: 10.1093/Nar/26.22.5212  1
1998 Bahar I, Jernigan RL. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. Journal of Molecular Biology. 281: 871-84. PMID 9719641 DOI: 10.1006/Jmbi.1998.1978  0.48
1998 Bahar I, Wallqvist A, Covell DG, Jernigan RL. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry. 37: 1067-75. PMID 9454598 DOI: 10.1021/Bi9720641  0.32
1997 Bahar I, Erman B, Haliloglu T, Jernigan RL. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry. 36: 13512-23. PMID 9354619 DOI: 10.1021/Bi971611F  0.44
1997 Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins. 29: 172-85. PMID 9329082 DOI: 10.1002/(Sici)1097-0134(199710)29:2<172::Aid-Prot5>3.0.Co;2-F  0.48
1997 Lustig B, Arora S, Jernigan RL. RNA base-amino acid interaction strengths derived from structures and sequences. Nucleic Acids Research. 25: 2562-5. PMID 9185564 DOI: 10.1093/Nar/25.13.2562  1
1997 Bahar I, Jernigan RL. Coordination geometry of nonbonded residues in globular proteins. Folding & Design. 1: 357-70. PMID 9080182 DOI: 10.1016/S1359-0278(96)00051-X  0.4
1997 Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. Journal of Molecular Biology. 266: 195-214. PMID 9054980 DOI: 10.1006/Jmbi.1996.0758  0.4
1996 Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Current Opinion in Structural Biology. 6: 195-209. PMID 8728652 DOI: 10.1016/S0959-440X(96)80075-3  0.36
1995 Lustig B, Jernigan RL. Consistencies of individual DNA base-amino acid interactions in structures and sequences. Nucleic Acids Research. 23: 4707-11. PMID 8524664 DOI: 10.1093/Nar/23.22.4707  1
1995 Lustig B, Lin NH, Smith SM, Jernigan RL, Jeang KT. A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation. Nucleic Acids Research. 23: 3531-8. PMID 7567466 DOI: 10.1093/Nar/23.17.3531  1
1994 Bahar I, Jernigan RL. Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. Biophysical Journal. 66: 467-81. PMID 8161700 DOI: 10.1016/S0006-3495(94)80798-2  0.48
1994 Bahar I, Jernigan RL. Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions. Biophysical Journal. 66: 454-66. PMID 8161699 DOI: 10.1016/S0006-3495(94)80797-0  0.52
1994 Layton AC, Lajoie CA, Easter JP, Jernigan R, Beck MJ, Sayler GS. Molecular diagnostics for polychlorinated biphenyl degradation in contaminated soils. Annals of the New York Academy of Sciences. 721: 407-22. PMID 8010689 DOI: 10.1111/J.1749-6632.1994.Tb47412.X  1
1994 Lustig B, Covell DG, Jernigan RL. Conformations of t-RNA: base pairing and stacking. Journal of Biomolecular Structure & Dynamics. 12: 145-61. PMID 7848564 DOI: 10.1080/07391102.1994.10508093  1
1994 Layton AC, Lajoie CA, Easter JP, Jernigan R, Sanseverino J, Sayler GS. Molecular diagnostics and chemical analysis for assessing biodegradation of polychlorinated biphenyls in contaminated soils. Journal of Industrial Microbiology. 13: 392-401. PMID 7765670 DOI: 10.1007/Bf01577225  1
1994 Jiang SP, Jernigan RL, Ting KL, Syi JL, Raghunathan G. Stability and cooperativity of nucleic acid base triplets. Journal of Biomolecular Structure & Dynamics. 12: 383-99. PMID 7702776 DOI: 10.1080/07391102.1994.10508747  1
1993 Olson WK, Marky NL, Jernigan RL, Zhurkin VB. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. Journal of Molecular Biology. 232: 530-54. PMID 8345522 DOI: 10.1006/Jmbi.1993.1409  1
1991 Zhurkin VB, Ulyanov NB, Gorin AA, Jernigan RL. Static and statistical bending of DNA evaluated by Monte Carlo simulations Proceedings of the National Academy of Sciences of the United States of America. 88: 7046-7050. PMID 1871119 DOI: 10.1073/Pnas.88.16.7046  1
1990 Ben-Naim A, Ting KL, Jernigan RL. Solvent effect on binding thermodynamics of biopolymers. Biopolymers. 29: 901-19. PMID 2369620 DOI: 10.1002/Bip.360290604  1
1989 Ben-Naim A, Ting KL, Jernigan RL. Solvation thermodynamics of biopolymers. II. Correlations between functional groups. Biopolymers. 28: 1327-37. PMID 2775845 DOI: 10.1002/Bip.360280712  1
1989 Ben-Naim A, Ting KL, Jernigan RL. Solvation thermodynamics of biopolymers. I. Separation of the volume and surface interactions with estimates for proteins. Biopolymers. 28: 1309-25. PMID 2775844 DOI: 10.1002/bip.360280711  1
1989 Jernigan R, Davies D, Scheraga H. Experimental and theoretical protein folding. Journal of Biomolecular Structure & Dynamics. 6: 1039-43. PMID 2684216 DOI: 10.1080/07391102.1989.10506534  0.01
1979 Bourgeois S, Jernigan RL, Szu SC, Kabat EA, Wu TT. Composite predictions of secondary structure of lac repressor Biopolymers. 18: 2625-2643. PMID 393316 DOI: 10.1002/Bip.1979.360181017  1
1969 Jernigan RL, Flory PJ. Distribution functions for chain molecules The Journal of Chemical Physics. 50: 4185-4200. DOI: 10.1063/1.1670884  1
1969 Jernigan RL, Flory PJ. Moments of chain vectors for models of polymer chains The Journal of Chemical Physics. 50: 4178-4185. DOI: 10.1063/1.1670883  1
1969 Jernigan RL, Flory PJ. Configurationl correlations in chain molecules The Journal of Chemical Physics. 50: 4165-4177. DOI: 10.1063/1.1670882  1
1968 Flory PJ, Jernigan RL. Kerr effect in polymer chains The Journal of Chemical Physics. 48: 3824-3825. DOI: 10.1063/1.1669691  1
1968 Flory PJ, Jernigan RL, Tonelli AE. Strain Birefringence of Polymer Chains The Journal of Chemical Physics. 48: 3822-3823. DOI: 10.1063/1.1669690  1
1968 Flory PJ, Jernigan RL. Rayleigh scattering by real chain molecules Journal of the American Chemical Society. 90: 3128-3134. DOI: 10.1021/ja01014a028  1
1967 Jernigan RL, Flory PJ. Optical Anisotropy of Chain Molecules. Theory of Depolarization of Scattered Light with Application ton‐Alkanes The Journal of Chemical Physics. 47: 1999-2007. DOI: 10.1063/1.1712228  1
1966 Abe A, Jernigan RL, Flory PJ. Conformational Energies of n-Alkanes and the Random Configuration of Higher Homologs Including Polymethylene Journal of the American Chemical Society. 88: 631-639. DOI: 10.1021/Ja00956A001  1
1965 Flory PJ, Jernigan RL. Second and Fourth Moments of Chain Molecules The Journal of Chemical Physics. 42: 3509-3519. DOI: 10.1063/1.1695753  1
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