| Year |
Citation |
Score |
| 2022 |
Khade PM, Jernigan RL. Entropies Derived from the Packing Geometries within a Single Protein Structure. Acs Omega. 7: 20719-20730. PMID 35755337 DOI: 10.1021/acsomega.2c00999 |
0.382 |
|
| 2022 |
Jernigan RL, Khade P, Kumar A, Kloczkowski A. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. Methods in Molecular Biology (Clifton, N.J.). 2340: 41-50. PMID 35167069 DOI: 10.1007/978-1-0716-1546-1_3 |
0.336 |
|
| 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 |
0.317 |
|
| 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 |
0.333 |
|
| 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 |
0.325 |
|
| 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 |
0.376 |
|
| 2020 |
Litterer BR, Jia K, Shome S, Jernigan RL. Using Sequence and Structure Information to Annotate Gene and Protein Function Biophysical Journal. 118: 44a. DOI: 10.1016/J.Bpj.2019.11.421 |
0.402 |
|
| 2020 |
Khade PM, Kumar A, Jernigan RL. Using Alpha Shapes to Characterize Protein Packing and Capture the Multiscale Aspects of Allostery Biophysical Journal. 118: 40a. DOI: 10.1016/J.Bpj.2019.11.401 |
0.314 |
|
| 2020 |
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Linking between Sequence, Structure, and Disorder Information Biophysical Journal. 118: 371a. DOI: 10.1016/J.Bpj.2019.11.2124 |
0.338 |
|
| 2019 |
Faraggi E, Dunker AK, Jernigan RL, Kloczkowski A. Entropy, Fluctuations, and Disordered Proteins. Entropy (Basel, Switzerland). 21. PMID 32336912 DOI: 10.3390/E21080764 |
0.344 |
|
| 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 |
0.52 |
|
| 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 |
0.394 |
|
| 2018 |
Jia K, Jernigan RL. Compensatory Mutations in Protein Sequences from Big-Data Biophysical Journal. 114: 574a-575a. DOI: 10.1016/J.Bpj.2017.11.3142 |
0.332 |
|
| 2018 |
Kumar Mishra S, Kandoi G, Jernigan RL. Dynamic Communities in Proteins: Allosteric Hotspots and Functional Modules Biophysical Journal. 114: 421a. DOI: 10.1016/J.Bpj.2017.11.2334 |
0.318 |
|
| 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 |
0.376 |
|
| 2017 |
Mishra SK, Sankar K, Jernigan RL. Altered Dynamics upon Oligomerization Corresponds to Key Functional Sites. Proteins. PMID 28383162 DOI: 10.1002/prot.25302 |
0.34 |
|
| 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 |
0.349 |
|
| 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 |
0.812 |
|
| 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 |
0.341 |
|
| 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 |
0.807 |
|
| 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 |
0.806 |
|
| 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 |
0.305 |
|
| 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 |
0.508 |
|
| 2016 |
Jernigan RL, Bahar I, Covell DG, Atilgan AR, Erman B, Flatow DT. Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step. Journal of Biomolecular Structure & Dynamics. 49-55. PMID 22607406 DOI: 10.1080/07391102.2000.10506603 |
0.645 |
|
| 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 |
0.47 |
|
| 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 |
0.418 |
|
| 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 |
0.78 |
|
| 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 |
0.815 |
|
| 2015 |
Zimmermann MT, Jia K, Jernigan RL. Ribosome Mechanics Informs about Mechanism Journal of Molecular Biology. DOI: 10.1016/j.jmb.2015.12.003 |
0.42 |
|
| 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 |
0.618 |
|
| 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 |
0.591 |
|
| 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 |
0.793 |
|
| 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 |
0.56 |
|
| 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 |
0.792 |
|
| 2013 |
Saraswathi S, Fernández-Martínez JL, Koliński A, Jernigan RL, Kloczkowski A. Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure. Journal of Molecular Modeling. 19: 4337-48. PMID 23907551 DOI: 10.1007/S00894-013-1911-Z |
0.471 |
|
| 2013 |
Jernigan RL. Possible alternative and extension to the use of dynamics for structure matching: comment on "Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments" by C. Micheletti. Physics of Life Reviews. 10: 37-8; discussion 39-. PMID 23394959 DOI: 10.1016/j.plrev.2013.01.013 |
0.306 |
|
| 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 |
0.399 |
|
| 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 |
0.512 |
|
| 2013 |
Jernigan RL, Liu J, Sankar K, Jia K, Zimmermann MT. 164 Extracting dynamics information from multiple structures Journal of Biomolecular Structure and Dynamics. 31: 106-107. DOI: 10.1080/07391102.2013.786406 |
0.626 |
|
| 2013 |
Leelananda SP, Jernigan RL. Incorporating Protein Topology Information in Similarity Matrices for Improved Sequence Matching (A Fold-Specific Scoring System) Biophysical Journal. 104: 508a. DOI: 10.1016/J.Bpj.2012.11.2804 |
0.803 |
|
| 2013 |
Katebi AR, Jernigan RL. Modeling Complex between FBA and TIM: Functional Motions of FBA and TIM are Preserved in their Complex Biophysical Journal. 104: 402a. DOI: 10.1016/J.Bpj.2012.11.2243 |
0.808 |
|
| 2013 |
Kloczkowski A, Gniewek P, Faraggi E, Zimmermann M, Gront D, Pawlowski M, Jernigan RL, Kolinski A. New Methods to Improve Protein Structure Prediction and Refinement Biophysical Journal. 104: 229a. DOI: 10.1016/J.Bpj.2012.11.1292 |
0.681 |
|
| 2013 |
Kasprzak WK, Afonin KA, Bindewald E, Puppala PS, Kim T, Zimmermann MT, Jernigan RL, Shapiro BA. Coarse-Grained Computational Characterization of RNA Nanocube Flexibility Correlates with Experiments Biophysical Journal. 104: 16a. DOI: 10.1016/J.Bpj.2012.11.119 |
0.57 |
|
| 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 |
0.629 |
|
| 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 |
0.499 |
|
| 2012 |
Saraswathi S, Fernández-Martínez JL, Kolinski A, Jernigan RL, Kloczkowski A. Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction. Journal of Molecular Modeling. 18: 4275-89. PMID 22562230 DOI: 10.1007/S00894-012-1410-7 |
0.444 |
|
| 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 |
0.822 |
|
| 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 |
0.793 |
|
| 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 |
0.397 |
|
| 2012 |
Zimmermann MT, Jernigan RL. Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein Entropy. 14: 687-700. DOI: 10.3390/E14040687 |
0.656 |
|
| 2012 |
Leelananda SP, Jernigan RL. Diversity of Sequences Folding to Highly and Poorly Designable Structures Biophysical Journal. 102: 456a. DOI: 10.1016/J.Bpj.2011.11.2500 |
0.811 |
|
| 2012 |
Burton B, Zimmerman MT, Jernigan RL, Wang Y. Linkage Between Dynamics and Assembly of Ribosomal Proteins Biophysical Journal. 102: 450a. DOI: 10.1016/J.Bpj.2011.11.2469 |
0.436 |
|
| 2012 |
Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. ANM Normal Modes Show the Directions for Protein Structure Refinement Biophysical Journal. 102: 25a. DOI: 10.1016/J.Bpj.2011.11.162 |
0.51 |
|
| 2012 |
Zimmermann MT, Jernigan RL. Computing Entropies for Binding and Refinement of Protein Structures Biophysical Journal. 102: 25a. DOI: 10.1016/J.Bpj.2011.11.161 |
0.666 |
|
| 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 |
0.59 |
|
| 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 |
0.587 |
|
| 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 |
0.814 |
|
| 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 |
0.82 |
|
| 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 |
0.579 |
|
| 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 |
0.47 |
|
| 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 |
0.806 |
|
| 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 |
0.354 |
|
| 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 |
0.544 |
|
| 2011 |
Kasprzak WK, Bindewald E, Kim T, Zimmermann MT, Jernigan RL, Shapiro BA. Design and Modeling of RNA Nanostructures with Flexible Building Blocks Biophysical Journal. 100: 472a. DOI: 10.1016/J.Bpj.2010.12.2766 |
0.598 |
|
| 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 |
0.44 |
|
| 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 |
0.543 |
|
| 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 |
0.79 |
|
| 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 |
0.458 |
|
| 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 |
0.69 |
|
| 2010 |
Jernigan RL, Miyazawa S, Szu SC. Electrostatic interactions and secondary structures in proteins. Biophysical Journal. 32: 93-5. PMID 19431420 DOI: 10.1016/S0006-3495(80)84926-5 |
0.423 |
|
| 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 |
0.472 |
|
| 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 |
0.813 |
|
| 2010 |
Sundararajan S, Gniewek P, Jernigan RL, Kolinski A, Kloczkowski A. Protein Secondary Structure Prediction Using Knowledge-Based Potentials and An Ensemble of Classifiers Biophysical Journal. 98: 52a. DOI: 10.1016/J.Bpj.2009.12.298 |
0.462 |
|
| 2010 |
Feng Y, Jernigan RL, Kloczkowski A. Multi-Body Knowledge-Based Potentials for Protein Structure Prediction Evaluation Biophysical Journal. 98: 392a. DOI: 10.1016/J.Bpj.2009.12.2115 |
0.708 |
|
| 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 |
0.313 |
|
| 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 |
0.365 |
|
| 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 |
0.643 |
|
| 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 |
0.46 |
|
| 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 |
0.443 |
|
| 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 |
0.413 |
|
| 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 |
0.636 |
|
| 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 |
0.499 |
|
| 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 |
0.425 |
|
| 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 |
0.358 |
|
| 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 |
0.439 |
|
| 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 |
0.433 |
|
| 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 |
0.649 |
|
| 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 |
0.763 |
|
| 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 |
0.671 |
|
| 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 |
0.365 |
|
| 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 |
0.434 |
|
| 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 |
0.655 |
|
| 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 |
0.666 |
|
| 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 |
0.777 |
|
| 2008 |
Kloczkowski A, Jernigan RL. Book Review of Molecular Modeling of Proteins. Methods in Molecular Biology, 443 Molecular Modeling of Proteins. Methods in Molecular Biology, 443 . Edited by Andreas Kukol (University of Hertfordshire, U.K.). Humana Press : Totowa . 2008. xii + 390 pp. $99.50. ISBN 978-1-58829-864-5 . Journal of the American Chemical Society. 130: 12548-12548. DOI: 10.1021/Ja805842D |
0.326 |
|
| 2008 |
Raghunathan G, Jernigan RL. Idealarchitecture of residue packing and itsobservationin proteinstructures Protein Science. 6: 2485-2485. DOI: 10.1002/Pro.5560061127 |
0.322 |
|
| 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 |
0.804 |
|
| 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 |
0.388 |
|
| 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 |
0.782 |
|
| 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 |
0.807 |
|
| 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 |
0.412 |
|
| 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 |
0.385 |
|
| 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 |
0.427 |
|
| 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 |
0.391 |
|
| 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 |
0.7 |
|
| 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 |
0.459 |
|
| 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 |
0.424 |
|
| 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 |
0.478 |
|
| 2007 |
Jernigan RL, Flory PJ. Configurational distributions for finite chain molecules Journal of Polymer Science Part C: Polymer Symposia. 25: 69-72. DOI: 10.1002/Polc.5070250109 |
0.414 |
|
| 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 |
0.759 |
|
| 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 |
0.349 |
|
| 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 |
0.789 |
|
| 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 |
0.628 |
|
| 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 |
0.644 |
|
| 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 |
0.406 |
|
| 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 |
0.768 |
|
| 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 |
0.372 |
|
| 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 |
0.385 |
|
| 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 |
0.802 |
|
| 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 |
0.436 |
|
| 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 |
0.375 |
|
| 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 |
0.329 |
|
| 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 |
0.337 |
|
| 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 |
0.63 |
|
| 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 |
0.302 |
|
| 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 |
0.375 |
|
| 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 |
0.359 |
|
| 2005 |
Kurkcuoglu O, Jernigan R, Doruker P. Collective Dynamics of Large Proteins from Mixed Coarse-Grained Elastic Network Model Qsar & Combinatorial Science. 24: 443-448. DOI: 10.1002/Qsar.200430922 |
0.426 |
|
| 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 |
0.67 |
|
| 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 |
0.521 |
|
| 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 |
0.421 |
|
| 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 |
0.413 |
|
| 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 |
0.409 |
|
| 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 |
0.33 |
|
| 2004 |
Kloczkowski A, Jernigan RL. Protein Conformational Computations-special issue of Polymer Polymer. 45: 507. DOI: 10.1016/J.Polymer.2003.10.074 |
0.318 |
|
| 2004 |
Kloczkowski A, Sen TZ, Jernigan RL. The transfer matrix method for lattice proteins—an application with cooperative interactions Polymer. 45: 707-716. DOI: 10.1016/J.Polymer.2003.10.072 |
0.633 |
|
| 2004 |
Kurkcuoglu O, Jernigan RL, Doruker P. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions Polymer. 45: 649-657. DOI: 10.1016/J.Polymer.2003.10.071 |
0.454 |
|
| 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 |
0.493 |
|
| 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 |
0.38 |
|
| 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 |
0.61 |
|
| 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 |
0.48 |
|
| 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 |
0.454 |
|
| 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 |
0.408 |
|
| 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 |
0.416 |
|
| 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 |
0.428 |
|
| 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 |
0.595 |
|
| 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 |
0.611 |
|
| 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 |
0.588 |
|
| 2002 |
Tolstorukov MY, Ivanov VI, Malenkov GG, Jernigan RL, Zhurkin VB. Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. Biophysical Journal. 81: 3409-21. PMID 11721003 DOI: 10.1016/S0006-3495(01)75973-5 |
0.342 |
|
| 2002 |
Bagci Z, Jernigan RL, Bahar I. Residue packing in proteins: Uniform distribution on a coarse-grained scale The Journal of Chemical Physics. 116: 2269-2276. DOI: 10.1063/1.1432502 |
0.632 |
|
| 2002 |
Bagci Z, Jernigan RL, Bahar I. Residue coordination in proteins conforms to the closest packing of spheres Polymer. 43: 451-459. DOI: 10.1016/S0032-3861(01)00427-X |
0.627 |
|
| 2002 |
Kloczkowski A, Ting K, Jernigan R, Garnier J. Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information Polymer. 43: 441-449. DOI: 10.1016/S0032-3861(01)00425-6 |
0.448 |
|
| 2002 |
Doruker P, Jernigan RL, Navizet I, Hernandez R. Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization International Journal of Quantum Chemistry. 90: 822-837. DOI: 10.1002/Qua.955 |
0.423 |
|
| 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 |
0.621 |
|
| 2000 |
Miyazawa S, Jernigan RL. Identifying sequence-structure pairs undetected by sequence alignments. Protein Engineering. 13: 459-75. PMID 10906342 DOI: 10.1093/Protein/13.7.459 |
0.458 |
|
| 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 |
0.474 |
|
| 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 |
0.583 |
|
| 1999 |
Miyazawa S, Jernigan RL. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins. 36: 357-69. PMID 10409829 DOI: 10.1002/(Sici)1097-0134(19990815)36:3<357::Aid-Prot10>3.0.Co;2-U |
0.49 |
|
| 1999 |
Miyazawa S, Jernigan RL. Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition. Proteins. 36: 347-56. PMID 10409828 DOI: 10.1002/(Sici)1097-0134(19990815)36:3<347::Aid-Prot9>3.0.Co;2-3 |
0.494 |
|
| 1999 |
Miyazawa S, Jernigan RL. Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins. 34: 49-68. PMID 10336383 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<49::Aid-Prot5>3.0.Co;2-L |
0.392 |
|
| 1999 |
Bahar I, Jernigan RL. Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry. 38: 3478-90. PMID 10090734 DOI: 10.1021/Bi982697V |
0.492 |
|
| 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 |
0.677 |
|
| 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 |
0.586 |
|
| 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 |
0.557 |
|
| 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 |
0.723 |
|
| 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 |
0.527 |
|
| 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 |
0.576 |
|
| 1998 |
Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB. A role for CH...O interactions in protein-DNA recognition. Journal of Molecular Biology. 277: 1129-40. PMID 9571027 DOI: 10.1006/Jmbi.1998.1660 |
0.325 |
|
| 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 |
0.591 |
|
| 1998 |
Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. 29: 292-308. PMID 9365985 DOI: 10.1002/(Sici)1097-0134(199711)29:3<292::Aid-Prot4>3.0.Co;2-D |
0.601 |
|
| 1998 |
Raghunathan G, Jernigan RL. Ideal architecture of residue packing and its observation in protein structures. Protein Science : a Publication of the Protein Society. 6: 2072-83. PMID 9336831 DOI: 10.1002/Pro.5560061003 |
0.443 |
|
| 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 |
0.668 |
|
| 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 |
0.688 |
|
| 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 |
0.353 |
|
| 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 |
0.557 |
|
| 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 |
0.6 |
|
| 1997 |
Sarai A, Jernigan RL, Mazur J. Interdependence of conformational variables in double-helical DNA. Biophysical Journal. 71: 1507-18. PMID 8874024 DOI: 10.1016/S0006-3495(96)79353-0 |
0.327 |
|
| 1997 |
Mazur J, Jernigan RL, Sarai A. Constructing optimal backbone segments for joining fixed DNA base pairs. Biophysical Journal. 71: 1493-506. PMID 8874023 DOI: 10.1016/S0006-3495(96)79352-9 |
0.354 |
|
| 1997 |
Erman B, Bahar I, Jernigan RL. Equilibrium states of rigid bodies with multiple interaction sites: Application to protein helices The Journal of Chemical Physics. 107: 2046-2059. DOI: 10.1063/1.474555 |
0.71 |
|
| 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 |
0.593 |
|
| 1996 |
Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. Journal of Molecular Biology. 256: 623-44. PMID 8604144 DOI: 10.1006/Jmbi.1996.0114 |
0.484 |
|
| 1996 |
Naor D, Fischer D, Jernigan RL, Wolfson HJ, Nussinov R. Amino acid pair interchanges at spatially conserved locations. Journal of Molecular Biology. 256: 924-38. PMID 8601843 DOI: 10.1006/Jmbi.1996.0138 |
0.432 |
|
| 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 |
0.359 |
|
| 1995 |
Miyazawa S, Jernigan RL. Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Engineering. 7: 1209-20. PMID 7855136 DOI: 10.1093/Protein/7.10.1209 |
0.366 |
|
| 1995 |
Mazur J, Jernigan RL. Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms. Biophysical Journal. 68: 1472-89. PMID 7787033 DOI: 10.1016/S0006-3495(95)80320-6 |
0.324 |
|
| 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 |
0.305 |
|
| 1994 |
Zhurkin VB, Raghunathan G, Ulyanov NB, Camerini-Otero RD, Jernigan RL. A parallel DNA triplex as a model for the intermediate in homologous recombination. Journal of Molecular Biology. 239: 181-200. PMID 8196053 DOI: 10.1006/Jmbi.1994.1362 |
0.319 |
|
| 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 |
0.527 |
|
| 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 |
0.462 |
|
| 1994 |
Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Science : a Publication of the Protein Society. 3: 717-29. PMID 8061602 DOI: 10.1002/Pro.5560030501 |
0.365 |
|
| 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 |
0.389 |
|
| 1994 |
Jernigan R, Raghunathan G, Bahar I. Characterization of interactions and metal ion binding sites in proteins Current Opinion in Structural Biology. 4: 256-263. DOI: 10.1016/S0959-440X(94)90317-4 |
0.558 |
|
| 1993 |
Miyazawa S, Jernigan RL. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Engineering. 6: 267-78. PMID 8506261 DOI: 10.1093/Protein/6.3.267 |
0.429 |
|
| 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 |
0.485 |
|
| 1992 |
Mazur J, Jernigan RL. Distance-dependent dielectric constants and their application to double-helical DNA. Biopolymers. 31: 1615-29. PMID 1814508 DOI: 10.1002/Bip.360311316 |
0.336 |
|
| 1992 |
Jernigan RL. Protein folds Current Biology. 2: 173. DOI: 10.1016/0960-9822(92)90504-4 |
0.303 |
|
| 1992 |
Jernigan RL. Protein folds Current Opinion in Structural Biology. 2: 248-256. DOI: 10.1016/0959-440X(92)90154-Y |
0.459 |
|
| 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 |
0.307 |
|
| 1991 |
Bohacek RS, Strauss UP, Jernigan RL. Configurational statistics of methyl vinyl ether-maleic anhydride copolymer: selection of important atomic interactions and conformations Macromolecules. 24: 731-739. DOI: 10.1021/Ma00003A016 |
0.317 |
|
| 1990 |
Jernigan RL, Sarai A, Shapiro B, Nussinov R. Relationship between curved DNA conformations and slow gel migration. Journal of Biomolecular Structure & Dynamics. 4: 561-7. PMID 3271455 DOI: 10.1080/07391102.1987.10507660 |
0.362 |
|
| 1990 |
Nussinov R, Sarai A, Smythers GW, Wang D, Jernigan RL. Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes. Journal of Biomolecular Structure & Dynamics. 7: 707-22. PMID 2627306 DOI: 10.1080/07391102.1989.10508515 |
0.307 |
|
| 1990 |
Sarai A, Mazur J, Nussinov R, Jernigan RL. Sequence dependence of DNA conformational flexibility. Biochemistry. 28: 7842-9. PMID 2611216 DOI: 10.1021/Bi00445A046 |
0.376 |
|
| 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 |
0.324 |
|
| 1990 |
Covell DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry. 29: 3287-94. PMID 2334692 DOI: 10.1021/Bi00465A020 |
0.45 |
|
| 1990 |
Sumner SC, Gallagher KS, Davis DG, Covell DG, Jernigan RL, Ferretti JA. Conformational analysis of the tachykinins in solution: substance P and physalaemin. Journal of Biomolecular Structure & Dynamics. 8: 687-707. PMID 1713036 DOI: 10.1080/07391102.1990.10507836 |
0.325 |
|
| 1989 |
Sarai A, Mazur J, Nussinov R, Jernigan RL. Origin of DNA helical structure and its sequence dependence. Biochemistry. 27: 8498-502. PMID 3242599 DOI: 10.1021/Bi00422A030 |
0.339 |
|
| 1989 |
Mazur J, Sarai A, Jernigan RL. Sequence dependence of the B-A conformational transition of DNA. Biopolymers. 28: 1223-33. PMID 2775837 DOI: 10.1002/Bip.360280704 |
0.343 |
|
| 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 |
0.397 |
|
| 1988 |
Margalit H, Shapiro BA, Nussinov R, Owens J, Jernigan RL. Helix stability in prokaryotic promoter regions. Biochemistry. 27: 5179-88. PMID 3167040 DOI: 10.1021/Bi00414A035 |
0.303 |
|
| 1986 |
Jernigan RL, Sarai A, Ting KL, Nussinov R. Hydrophobic interactions in the major groove can influence DNA local structure. Journal of Biomolecular Structure & Dynamics. 4: 41-8. PMID 3271434 DOI: 10.1080/07391102.1986.10507645 |
0.36 |
|
| 1985 |
Church WR, Jernigan RL, Toole J, Hewick RM, Knopf J, Knutson GJ, Nesheim ME, Mann KG, Fass DN. Coagulation factors V and VIII and ceruloplasmin constitute a family of structurally related proteins. Proceedings of the National Academy of Sciences of the United States of America. 81: 6934-7. PMID 6438625 DOI: 10.1073/Pnas.81.22.6934 |
0.353 |
|
| 1985 |
Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation Macromolecules. 18: 534-552. DOI: 10.1021/Ma00145A039 |
0.361 |
|
| 1984 |
Jernigan RL, Miyazawa S. Equilibrium folding-unfolding pathways of model proteins: effect of myoglobin-heme contacts. Biopolymers. 22: 79-85. PMID 6673775 DOI: 10.1002/Bip.360220113 |
0.375 |
|
| 1983 |
Miyazawa S, Jernigan RL. Most probable intermediates in protein folding-unfolding with a noninteracting globule-coil model. Biochemistry. 21: 5203-13. PMID 7171549 DOI: 10.1021/Bi00264A015 |
0.418 |
|
| 1983 |
Miyazawa S, Jernigan RL. Equilibrium folding pathways for model proteins Journal of Statistical Physics. 30: 549-559. DOI: 10.1007/Bf01012328 |
0.391 |
|
| 1982 |
Miyazawa S, Jernigan RL. Equilibrium folding and unfolding pathways for a model protein. Biopolymers. 21: 1333-63. PMID 7115893 DOI: 10.1002/Bip.360210706 |
0.39 |
|
| 1980 |
Jernigan RL, Miyazawa S, Szu SC. Stabilization of Regular Conformational Regions in Proteins by Intraregion Electrostatic Interactions Macromolecules. 13: 518-525. DOI: 10.1021/Ma60075A010 |
0.381 |
|
| 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 |
0.376 |
|
| 1978 |
Wu TT, Szu SC, Jernigan RL, Bilofsky H, Kabat EA. Prediction of ?-sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 � 20 table for evaluation of the effects of nearest-neighbors on conformations of middle amino acids in proteins Biopolymers. 17: 555-572. DOI: 10.1002/Bip.1978.360170303 |
0.392 |
|
| 1973 |
Ferretti JA, Jernigan RL, Weiss GH. Polypeptide helix lifetimes in the helix-random coil transition region. Application to NMR spectra Journal of Polymer Science: Polymer Symposia. 42: 1051-1059. DOI: 10.1002/Polc.5070420255 |
0.308 |
|
| 1969 |
Jernigan RL, Flory PJ. Distribution functions for chain molecules The Journal of Chemical Physics. 50: 4185-4200. DOI: 10.1063/1.1670884 |
0.377 |
|
| 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 |
0.377 |
|
| 1969 |
Jernigan RL, Flory PJ. Configurationl correlations in chain molecules The Journal of Chemical Physics. 50: 4165-4177. DOI: 10.1063/1.1670882 |
0.372 |
|
| 1968 |
Flory PJ, Jernigan RL. Kerr effect in polymer chains The Journal of Chemical Physics. 48: 3824-3825. DOI: 10.1063/1.1669691 |
0.349 |
|
| 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 |
0.504 |
|
| 1968 |
Flory PJ, Jernigan RL. Rayleigh scattering by real chain molecules Journal of the American Chemical Society. 90: 3128-3134. DOI: 10.1021/ja01014a028 |
0.363 |
|
| 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 |
0.349 |
|
| 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 |
0.483 |
|
| 1965 |
Leonard WJ, Jernigan RL, Flory PJ. Dipole Moments in Relation to Configuration of n‐Alkane Chains Bearing α, ω Dipolar Substituents The Journal of Chemical Physics. 43: 2256-2261. DOI: 10.1063/1.1697119 |
0.434 |
|
| 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 |
0.373 |
|
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