| Year |
Citation |
Score |
| 2019 |
Egli M, Lybrand TP. Enhanced Dispersion and Polarization Interactions Achieved through Dithiophosphate Group Incorporation Yield a Dramatic Binding Affinity Increase for an RNA Aptamer-Thrombin Complex. Journal of the American Chemical Society. PMID 30794399 DOI: 10.1021/Jacs.9B00104 |
0.344 |
|
| 2018 |
Sárosi MB, Lybrand TP. Molecular dynamics simulation of cyclooxygenase-2 complexes with indomethacin closo-carborane analogs. Journal of Chemical Information and Modeling. PMID 30067351 DOI: 10.1021/Acs.Jcim.8B00275 |
0.383 |
|
| 2017 |
Sárosi MB, Neumann W, Lybrand TP, Hey-Hawkins E. Molecular Modeling of the Interactions Between Carborane-Containing Analogs of Indomethacin and Cyclooxygenase-2. Journal of Chemical Information and Modeling. PMID 28632381 DOI: 10.1021/Acs.Jcim.7B00113 |
0.432 |
|
| 2016 |
Baugh L, Le Trong I, Stayton PS, Stenkamp RE, Lybrand TP. A Streptavidin Binding Site Mutation Yields an Unexpected Result: An Ionized Asp128 Residue is Not Essential for Strong Biotin Binding. Biochemistry. PMID 27603565 DOI: 10.1021/Acs.Biochem.6B00698 |
0.412 |
|
| 2016 |
Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, ... Lybrand TP, et al. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Research. PMID 27566147 DOI: 10.1093/Nar/Gkw725 |
0.371 |
|
| 2015 |
Konkle ME, Blobaum AL, Moth CW, Prusakiewicz JJ, Xu S, Ghebreselasie K, Akingbade D, Jacobs AT, Rouzer CA, Lybrand TP, Marnett LJ. A Conservative Secondary Shell Substitution In Cyclooxygenase-2 Reduces Inhibition by Indomethacin Amides and Esters via Altered Enzyme Dynamics. Biochemistry. PMID 26704937 DOI: 10.1021/Acs.Biochem.5B01222 |
0.768 |
|
| 2015 |
Weber DK, Yao S, Rojko N, Anderluh G, Lybrand TP, Downton MT, Wagner J, Separovic F. Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation. Biophysical Journal. 108: 1987-96. PMID 25902438 DOI: 10.1016/J.Bpj.2015.03.024 |
0.388 |
|
| 2015 |
Sani M, Lybrand TP, Separovic F. Structure and Membrane Topology of the Pore-Forming Peptide Maculatin 1.1 Biophysical Journal. 108: 549a. DOI: 10.1016/J.Bpj.2014.11.3014 |
0.316 |
|
| 2014 |
Stow SM, Goodwin CR, Kliman M, Bachmann BO, McLean JA, Lybrand TP. Distance geometry protocol to generate conformations of natural products to structurally interpret ion mobility-mass spectrometry collision cross sections. The Journal of Physical Chemistry. B. 118: 13812-20. PMID 25360896 DOI: 10.1021/Jp509398E |
0.313 |
|
| 2014 |
Edwards SJ, Moth CW, Kim S, Brandon S, Zhou Z, Cobb CE, Hustedt EJ, Beth AH, Smith JA, Lybrand TP. Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex. The Journal of Physical Chemistry. B. 118: 4717-26. PMID 24758720 DOI: 10.1021/Jp4099705 |
0.752 |
|
| 2014 |
Weber D, Yao S, Anderluh G, Lybrand T, Downton M, Wagner J, Separovic F. Modelling the Interactions of Equinatoxin II with Micelles Biophysical Journal. 106: 297a. DOI: 10.1016/J.Bpj.2013.11.566 |
0.373 |
|
| 2013 |
Smith JA, Edwards SJ, Moth CW, Lybrand TP. TagDock: an efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning. Biochemistry. 52: 5577-84. PMID 23875708 DOI: 10.1021/Bi400158K |
0.758 |
|
| 2013 |
Le Trong I, Chu V, Xing Y, Lybrand TP, Stayton PS, Stenkamp RE. Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin. Acta Crystallographica. Section D, Biological Crystallography. 69: 968-77. PMID 23695241 DOI: 10.1107/S0907444913003855 |
0.4 |
|
| 2012 |
Baugh L, Le Trong I, Cerutti DS, Mehta N, Gülich S, Stayton PS, Stenkamp RE, Lybrand TP. Second-contact shell mutation diminishes streptavidin-biotin binding affinity through transmitted effects on equilibrium dynamics. Biochemistry. 51: 597-607. PMID 22145986 DOI: 10.1021/Bi201221J |
0.397 |
|
| 2011 |
Le Trong I, Wang Z, Hyre DE, Lybrand TP, Stayton PS, Stenkamp RE. Streptavidin and its biotin complex at atomic resolution. Acta Crystallographica. Section D, Biological Crystallography. 67: 813-21. PMID 21904034 DOI: 10.1107/S0907444911027806 |
0.397 |
|
| 2011 |
Kim S, Brandon S, Zhou Z, Cobb CE, Edwards SJ, Moth CW, Parry CS, Smith JA, Lybrand TP, Hustedt EJ, Beth AH. Determination of structural models of the complex between the cytoplasmic domain of erythrocyte band 3 and ankyrin-R repeats 13-24. The Journal of Biological Chemistry. 286: 20746-57. PMID 21493712 DOI: 10.1074/Jbc.M111.230326 |
0.758 |
|
| 2011 |
Kim S, Brandon S, Smith JA, Edwards SJ, Lybrand TP, Cobb CE, Hustedt EJ, Beth AH. Site-Directed Spin-Labeling Studies: Structure of the AnkD34-Cdb3 Complex Biophysical Journal. 100: 145a. DOI: 10.1016/J.Bpj.2010.12.996 |
0.404 |
|
| 2010 |
Baugh L, Le Trong I, Cerutti DS, Gülich S, Stayton PS, Stenkamp RE, Lybrand TP. A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects? Biochemistry. 49: 4568-70. PMID 20462252 DOI: 10.1021/Bi1005392 |
0.401 |
|
| 2009 |
Muppirala UK, Desensi S, Lybrand TP, Hazelbauer GL, Li Z. Molecular modeling of flexible arm-mediated interactions between bacterial chemoreceptors and their modification enzyme. Protein Science : a Publication of the Protein Society. 18: 1702-14. PMID 19606502 DOI: 10.1002/Pro.170 |
0.756 |
|
| 2009 |
Cerutti DS, Le Trong I, Stenkamp RE, Lybrand TP. Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations. The Journal of Physical Chemistry. B. 113: 6971-85. PMID 19374419 DOI: 10.1021/Jp9010372 |
0.306 |
|
| 2009 |
Kazmier KN, Lybrand TP, Hustedt EJ. Calculation of the EPR Spectrum of a Small Nitroxide from Molecular Dynamics Simulations Biophysical Journal. 96: 310a-311a. DOI: 10.1016/J.Bpj.2008.12.1549 |
0.36 |
|
| 2008 |
Cerutti DS, Duke R, Freddolino PL, Fan H, Lybrand TP. Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. Journal of Chemical Theory and Computation. 4: 1669-1680. PMID 19180249 DOI: 10.1021/Ct8002173 |
0.343 |
|
| 2008 |
Cerutti DS, Le Trong I, Stenkamp RE, Lybrand TP. Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex. Biochemistry. 47: 12065-77. PMID 18950193 DOI: 10.1021/Bi800894U |
0.312 |
|
| 2008 |
Felts AS, Siegel BS, Young SM, Moth CW, Lybrand TP, Dannenberg AJ, Marnett LJ, Subbaramaiah K. Sulindac derivatives that activate the peroxisome proliferator-activated receptor gamma but lack cyclooxygenase inhibition. Journal of Medicinal Chemistry. 51: 4911-9. PMID 18665581 DOI: 10.1021/Jm700969C |
0.753 |
|
| 2008 |
DeSensi SC, Rangel DP, Beth AH, Lybrand TP, Hustedt EJ. Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations. Biophysical Journal. 94: 3798-809. PMID 18234808 DOI: 10.1529/Biophysj.107.125419 |
0.743 |
|
| 2007 |
Rigsby RE, Brown DW, Dawson E, Lybrand TP, Armstrong RN. A model for glutathione binding and activation in the fosfomycin resistance protein, FosA. Archives of Biochemistry and Biophysics. 464: 277-83. PMID 17537395 DOI: 10.1016/J.Abb.2007.04.035 |
0.384 |
|
| 2006 |
Harikumar KG, Dong M, Cheng Z, Pinon DI, Lybrand TP, Miller LJ. Transmembrane segment peptides can disrupt cholecystokinin receptor oligomerization without affecting receptor function. Biochemistry. 45: 14706-16. PMID 17144663 DOI: 10.1021/Bi061107N |
0.355 |
|
| 2006 |
Furse KE, Pratt DA, Schneider C, Brash AR, Porter NA, Lybrand TP. Molecular dynamics simulations of arachidonic acid-derived pentadienyl radical intermediate complexes with COX-1 and COX-2: insights into oxygenation regio- and stereoselectivity. Biochemistry. 45: 3206-18. PMID 16519515 DOI: 10.1021/Bi052338H |
0.766 |
|
| 2006 |
Furse KE, Pratt DA, Porter NA, Lybrand TP. Molecular dynamics simulations of arachidonic acid complexes with COX-1 and COX-2: insights into equilibrium behavior. Biochemistry. 45: 3189-205. PMID 16519514 DOI: 10.1021/Bi052337P |
0.773 |
|
| 2006 |
Hadac EM, Dawson ES, Darrow JW, Sugg EE, Lybrand TP, Miller LJ. Novel benzodiazepine photoaffinity probe stereoselectively labels a site deep within the membrane-spanning domain of the cholecystokinin receptor. Journal of Medicinal Chemistry. 49: 850-63. PMID 16451051 DOI: 10.1021/Jm049072H |
0.444 |
|
| 2005 |
Hata AN, Lybrand TP, Breyer RM. Identification of determinants of ligand binding affinity and selectivity in the prostaglandin D2 receptor CRTH2. The Journal of Biological Chemistry. 280: 32442-51. PMID 16030019 DOI: 10.1074/Jbc.M502563200 |
0.423 |
|
| 2005 |
Moth CW, Prusakiewicz JJ, Marnett LJ, Lybrand TP. Stereoselective binding of indomethacin ethanolamide derivatives to cyclooxygenase-1 Journal of Medicinal Chemistry. 48: 3613-3620. PMID 15887968 DOI: 10.1021/Jm0494164 |
0.781 |
|
| 2005 |
Hata AN, Lybrand TP, Marnett LJ, Breyer RM. Structural determinants of arylacetic acid nonsteroidal anti-inflammatory drugs necessary for binding and activation of the prostaglandin D2 receptor CRTH2 Molecular Pharmacology. 67: 640-647. PMID 15563582 DOI: 10.1124/Mol.104.007971 |
0.435 |
|
| 2004 |
Harikumar KG, Pinon DI, Wessels WS, Dawson ES, Lybrand TP, Prendergast FG, Miller LJ. Measurement of intermolecular distances for the natural agonist Peptide docked at the cholecystokinin receptor expressed in situ using fluorescence resonance energy transfer. Molecular Pharmacology. 65: 28-35. PMID 14722234 DOI: 10.1124/Mol.65.1.28 |
0.436 |
|
| 2004 |
Dong M, Li Z, Pinon DI, Lybrand TP, Miller LJ. Spatial approximation between the amino terminus of a peptide agonist and the top of the sixth transmembrane segment of the secretin receptor. The Journal of Biological Chemistry. 279: 2894-903. PMID 14593094 DOI: 10.1074/Jbc.M310407200 |
0.424 |
|
| 2003 |
Furse KE, Lybrand TP. Three-dimensional models for beta-adrenergic receptor complexes with agonists and antagonists. Journal of Medicinal Chemistry. 46: 4450-62. PMID 14521408 DOI: 10.1021/Jm0301437 |
0.767 |
|
| 2003 |
Dong M, Li Z, Zang M, Pinon DI, Lybrand TP, Miller LJ. Spatial approximation between two residues in the mid-region of secretin and the amino terminus of its receptor. Incorporation of seven sets of such constraints into a three-dimensional model of the agonist-bound secretin receptor. The Journal of Biological Chemistry. 278: 48300-12. PMID 14500709 DOI: 10.1074/Jbc.M309166200 |
0.424 |
|
| 2003 |
Zang M, Dong M, Pinon DI, Ding XQ, Hadac EM, Li Z, Lybrand TP, Miller LJ. Spatial approximation between a photolabile residue in position 13 of secretin and the amino terminus of the secretin receptor. Molecular Pharmacology. 63: 993-1001. PMID 12695527 DOI: 10.1124/Mol.63.5.993 |
0.435 |
|
| 2003 |
Zang M, Dong M, Pinon DI, Ding XQ, Hadac EM, Li Z, Lybrand TP, Miller LJ. Erratum: Spatial approximation between a photolabile residue in position 13 of secretin and the amino terminus of the secretin receptor (Molecular Pharmacology (2003) 63 (993-1001)) Molecular Pharmacology. 64. DOI: 10.1124/Mol.64.1.193 |
0.347 |
|
| 2002 |
Dawson ES, Henne RM, Miller LJ, Lybrand TP. Moleular models for cholecystokinin-A receptor. Pharmacology & Toxicology. 91: 290-6. PMID 12688371 DOI: 10.1034/J.1600-0773.2002.910605.X |
0.391 |
|
| 2002 |
Miller LJ, Lybrand TP. Molecular basis of agonist binding to the type A cholecystokinin receptor. Pharmacology & Toxicology. 91: 282-5. PMID 12688369 DOI: 10.1034/J.1600-0773.2002.910603.X |
0.43 |
|
| 2002 |
Dong M, Zang M, Pinon DI, Li Z, Lybrand TP, Miller LJ. Interaction among four residues distributed through the secretin pharmacophore and a focused region of the secretin receptor amino terminus. Molecular Endocrinology (Baltimore, Md.). 16: 2490-501. PMID 12403838 DOI: 10.1210/Me.2002-0111 |
0.424 |
|
| 2002 |
Hyre DE, Amon LM, Penzotti JE, Le Trong I, Stenkamp RE, Lybrand TP, Stayton PS. Early mechanistic events in biotin dissociation from streptavidin. Nature Structural Biology. 9: 582-5. PMID 12134141 DOI: 10.1038/Nsb825 |
0.315 |
|
| 2002 |
Ding XQ, Pinon DI, Furse KE, Lybrand TP, Miller LJ. Refinement of the conformation of a critical region of charge-charge interaction between cholecystokinin and its receptor. Molecular Pharmacology. 61: 1041-52. PMID 11961122 DOI: 10.1124/mol.61.5.1041 |
0.777 |
|
| 2002 |
Peach ML, Hazelbauer GL, Lybrand TP. Modeling the transmembrane domain of bacterial chemoreceptors. Protein Science : a Publication of the Protein Society. 11: 912-23. PMID 11910034 DOI: 10.1110/Ps.4640102 |
0.336 |
|
| 2001 |
Ding XQ, Dolu V, Hadac EM, Holicky EL, Pinon DI, Lybrand TP, Miller LJ. Refinement of the structure of the ligand-occupied cholecystokinin receptor using a photolabile amino-terminal probe. The Journal of Biological Chemistry. 276: 4236-44. PMID 11050076 DOI: 10.1074/Jbc.M003798200 |
0.415 |
|
| 1999 |
Stayton PS, Freitag S, Klumb LA, Chilkoti A, Chu V, Penzotti JE, To R, Hyre D, Le Trong I, Lybrand TP, Stenkamp RE. Streptavidin-biotin binding energetics. Biomolecular Engineering. 16: 39-44. PMID 10796983 DOI: 10.1016/S1050-3862(99)00042-X |
0.4 |
|
| 1999 |
McFarland BJ, Sant AJ, Lybrand TP, Beeson C. Ovalbumin(323-339) peptide binds to the major histocompatibility complex class II I-A(d) protein using two functionally distinct registers. Biochemistry. 38: 16663-70. PMID 10600129 DOI: 10.1021/Bi991393L |
0.302 |
|
| 1999 |
Freitag S, Chu V, Penzotti JE, Klumb LA, To R, Hyre D, Le Trong I, Lybrand TP, Stenkamp RE, Stayton PS. A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway. Proceedings of the National Academy of Sciences of the United States of America. 96: 8384-9. PMID 10411884 DOI: 10.1073/Pnas.96.15.8384 |
0.328 |
|
| 1999 |
Hadac EM, Ji Z, Pinon DI, Henne RM, Lybrand TP, Miller LJ. A peptide agonist acts by occupation of a monomeric G protein-coupled receptor: dual sites of covalent attachment to domains near TM1 and TM7 of the same molecule make biologically significant domain-swapped dimerization unlikely. Journal of Medicinal Chemistry. 42: 2105-11. PMID 10377216 DOI: 10.1021/Jm980732Q |
0.404 |
|
| 1998 |
Hjelmström P, Penzotti JE, Henne RM, Lybrand TP. A molecular model of myelin oligodendrocyte glycoprotein. Journal of Neurochemistry. 71: 1742-9. PMID 9751210 DOI: 10.1046/J.1471-4159.1998.71041742.X |
0.373 |
|
| 1998 |
Hjelmström P, DeWeese-Scott C, Penzotti JE, Lybrand TP, Sanjeevi CB. Structural differences between HLA-DQ molecules associated with myasthenia gravis characterized by molecular modeling. Journal of Neuroimmunology. 85: 102-5. PMID 9627003 DOI: 10.1016/S0165-5728(97)00266-X |
0.316 |
|
| 1998 |
Hadac EM, Pinon DI, Ji Z, Holicky EL, Henne RM, Lybrand TP, Miller LJ. Direct identification of a second distinct site of contact between cholecystokinin and its receptor. The Journal of Biological Chemistry. 273: 12988-93. PMID 9582333 DOI: 10.1074/Jbc.273.21.12988 |
0.389 |
|
| 1998 |
Hamaguchi N, True TA, Goetz AS, Stouffer MJ, Lybrand TP, Jeffs PW. Alpha 1-adrenergic receptor subtype determinants for 4-piperidyl oxazole antagonists. Biochemistry. 37: 5730-7. PMID 9548959 DOI: 10.1021/Bi972733A |
0.3 |
|
| 1998 |
Hadac E, Pinon D, Ji Z, Holicky E, Lybrand T, Miller L. Intrinsic photoaffinity labeling of the cholecystokinin receptor provides dual constraints for modeling the ligand-binding site Gastroenterology. 114: A466. DOI: 10.1016/S0016-5085(98)81885-4 |
0.437 |
|
| 1997 |
Ji Z, Hadac EM, Henne RM, Patel SA, Lybrand TP, Miller LJ. Direct identification of a distinct site of interaction between the carboxyl-terminal residue of cholecystokinin and the type A cholecystokinin receptor using photoaffinity labeling. The Journal of Biological Chemistry. 272: 24393-401. PMID 9305898 DOI: 10.1074/Jbc.272.39.24393 |
0.464 |
|
| 1997 |
Penzotti JE, Nepom GT, Lybrand TP. Use of T cell receptor/HLA-DRB1*04 molecular modeling to predict site-specific interactions for the DR shared epitope associated with rheumatoid arthritis. Arthritis and Rheumatism. 40: 1316-26. PMID 9214433 DOI: 10.1002/1529-0131(199707)40:7<1316::Aid-Art17>3.0.Co;2-I |
0.341 |
|
| 1996 |
Kontoyianni M, DeWeese C, Penzotti JE, Lybrand TP. Three-dimensional models for agonist and antagonist complexes with beta 2 adrenergic receptor. Journal of Medicinal Chemistry. 39: 4406-20. PMID 8893835 DOI: 10.1021/Jm960241A |
0.386 |
|
| 1996 |
Penzotti JE, Doherty D, Lybrand TP, Nepom GT. A structural model for TCR recognition of the HLA class II shared epitope sequence implicated in susceptibility to rheumatoid arthritis. Journal of Autoimmunity. 9: 287-93. PMID 8738976 DOI: 10.1006/Jaut.1996.0037 |
0.306 |
|
| 1996 |
Annand RR, Kontoyianni M, Penzotti JE, Dudler T, Lybrand TP, Gelb MH. Active site of bee venom phospholipase A2: the role of histidine-34, aspartate-64 and tyrosine-87. Biochemistry. 35: 4591-601. PMID 8605210 DOI: 10.1021/Bi9528412 |
0.306 |
|
| 1996 |
DeWeese C, Kwok WW, Nepom GT, Lybrand TP. Characterization of a Novel Reverse-orientation Model for a Peptide/MHC Complex Putatively Associated with Type I Diabetes Mellitus Journal of Molecular Modeling. 2: 205-216. DOI: 10.1007/S0089460020205 |
0.339 |
|
| 1995 |
Sanjeevi CB, Lybrand TP, DeWeese C, Landin-Olsson M, Kockum I, Dahlquist G, Sundkvist G, Stenger D, Lernmark A. Polymorphic amino acid variations in HLA-DQ are associated with systematic physical property changes and occurrence of IDDM. Members of the Swedish Childhood Diabetes Study. Diabetes. 44: 125-31. PMID 7813806 DOI: 10.2337/Diab.44.1.125 |
0.307 |
|
| 1995 |
Lybrand TP. Ligand-protein docking and rational drug design. Current Opinion in Structural Biology. 5: 224-8. PMID 7648325 DOI: 10.1016/0959-440X(95)80080-8 |
0.356 |
|
| 1993 |
Kontoyianni M, Lybrand TP. Three-dimensional models for integral membrane proteins: Possibilities and pitfalls Perspectives in Drug Discovery and Design. 1: 291-300. DOI: 10.1007/Bf02174530 |
0.304 |
|
| 1992 |
MaloneyHuss K, Lybrand TP. Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies. Journal of Molecular Biology. 225: 859-71. PMID 1318386 DOI: 10.1016/0022-2836(92)90406-A |
0.344 |
|
| 1990 |
Mazor MH, McCammon JA, Lybrand TP. Molecular recognition in nonaqueous solvent. 2. Structural and thermodynamic analysis of cationic selectivity of 18-crown-6 in methanol Journal of the American Chemical Society. 112: 4411-4419. DOI: 10.1021/Ja00167A044 |
0.314 |
|
| 1989 |
Rao SN, Lybrand T, Michaud D, Jerina DM, Kollman PA. Molecular mechanics simulations on covalent complexes between polycyclic carcinogens and B-DNA. Carcinogenesis. 10: 27-38. PMID 2910528 DOI: 10.1093/Carcin/10.1.27 |
0.338 |
|
| 1986 |
Lybrand TP, Kollman PA, Yu VC, Sadée W. Conformation and electrostatic potential surfaces of opiates: Relationship to µ- and λ-site binding. Pharmaceutical Research. 3: 218-24. PMID 24271585 DOI: 10.1023/A:1016338730077 |
0.302 |
|
| 1981 |
Lybrand T, Dearing A, Weiner P, Kollman P. A molecular mechanical study of complexes formed between 4-nitroquinoline-N-oxide and dinucleoside phosphates. Nucleic Acids Research. 9: 6995-7011. PMID 6801629 DOI: 10.1093/Nar/9.24.6995 |
0.333 |
|
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