Robert L. Jernigan - Publications

Iowa State University, Ames, IA, United States 

86 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
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  0.72
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  0.36
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  0.48
2017 Mishra SK, Sankar K, Jernigan RL. Altered Dynamics upon Oligomerization Corresponds to Key Functional Sites. Proteins. PMID 28383162 DOI: 10.1002/prot.25302  0.36
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  0.36
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  0.76
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  0.36
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  0.88
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  0.88
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  0.72
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  0.4
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  0.48
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
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  0.68
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  0.72
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  0.72
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  0.68
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  0.68
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  0.68
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  0.68
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  0.88
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  0.88
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  0.68
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  0.88
2011 Zimmermann MT, Skliros A, Kloczkowski A, Jernigan RL. Immunoglobulin Structure Exhibits Control over CDR Motion. Immunome Research. 7. PMID 25191522  0.68
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  0.88
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  0.88
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  0.88
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  0.68
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  0.88
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  0.72
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  0.68
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  0.68
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  0.4
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  0.88
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  0.88
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  0.4
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  0.68
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  0.72
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  0.88
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  0.88
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  0.72
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  0.76
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  0.68
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  0.88
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  0.88
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  0.88
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  0.88
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  0.72
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  0.88
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  0.88
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  0.68
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  0.88
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  0.88
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  0.88
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  0.88
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  0.68
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  0.68
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  0.72
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  0.88
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  0.88
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  0.88
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  0.68
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  0.88
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  0.88
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  0.88
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  0.68
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  0.48
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  0.76
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  0.68
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  0.68
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  0.48
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  0.88
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  0.68
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  0.88
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  0.68
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  0.68
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  0.76
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  0.88
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  0.88
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  0.84
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  0.84
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  0.32
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