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Stephen K. Burley, M.D., D.Phil. - Related publications

2002 Rockefeller University, New York, NY, United States 
 2012- Rutgers University, New Brunswick, NJ, United States 
General Biophysics, Molecular Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Benini S, Haouz A, Proux F, Alzari P, Wilson K. The crystal structure of Rv2991 from Mycobacterium tuberculosis: an F binding protein with unknown function. Journal of Structural Biology. PMID 30890426 DOI: 10.1016/j.jsb.2019.03.006   
2019 Camara-Artigas A, Murciano-Calles J, Martínez JC. Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95. Acta Crystallographica. Section D, Structural Biology. 75: 381-391. PMID 30988255 DOI: 10.1107/S2059798319001980   
2019 Ghosh P, Bhattacharyya T, Mathew OK, Sowdhamini R. PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. Database : the Journal of Biological Databases and Curation. 2019. PMID 30820573 DOI: 10.1093/database/baz028   
2019 Zhang J, Nanjaraj Urs AN, Lin L, Zhou Y, Hu Y, Hua G, Gao Q, Yuchi Z, Zhang Y. Structure of glycerol dehydrogenase (GldA) from Escherichia coli. Acta Crystallographica. Section F, Structural Biology Communications. 75: 176-183. PMID 30839292 DOI: 10.1107/S2053230X19000037   
2019 Furlong EJ, Kurth F, Premkumar L, Whitten AE, Martin JL. Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis. Acta Crystallographica. Section D, Structural Biology. 75: 296-307. PMID 30950400 DOI: 10.1107/S2059798319000081   
2019 Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallographica. Section D, Structural Biology. 75: 123-137. PMID 30821702 DOI: 10.1107/S2059798318017941   
2019 Modi V, Dunbrack RL. Defining a new nomenclature for the structures of active and inactive kinases. Proceedings of the National Academy of Sciences of the United States of America. PMID 30867294 DOI: 10.1073/pnas.1814279116   
2019 Li Z, Wu D, Zhan B, Hu X, Gan J, Ji C, Li J. Structural insights into the complex of trigger factor chaperone and ribosomal protein S7 from Mycobacterium tuberculosis. Biochemical and Biophysical Research Communications. PMID 30928093 DOI: 10.1016/j.bbrc.2019.03.166   
2019 Qi HW, Kulik HJ. Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis. Journal of Chemical Information and Modeling. PMID 30875210 DOI: 10.1021/acs.jcim.9b00144   
2019 Tripler TN, Kaplan AR, Alexandrescu AT, Teschke CM. Conservation and divergence of the I-domain inserted into the ubiquitous HK97 coat protein fold in the P22-like bacteriophages. Journal of Virology. PMID 30787158 DOI: 10.1128/JVI.00007-19   
2019 Munshi S, Subramanian S, Ramesh S, Golla H, Kalivarathan D, Kulkarni M, Campos Prieto LA, Sekhar A, Naganathan AN. Engineering Order and Cooperativity in a Disordered Protein. Biochemistry. PMID 31002232 DOI: 10.1021/acs.biochem.9b00182   
2019 Maniaci B, Lipper CH, Anipindi LD, Erlandsen H, Cole JL, Stec B, Huxford T, Love JJ. Design of High-Affinity Metal-Controlled Protein Dimers. Biochemistry. PMID 30938154 DOI: 10.1021/acs.biochem.9b00055   
2019 Estaña A, Ghallab M, Bernadó P, Cortés J. Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm. Molecules (Basel, Switzerland). 24. PMID 30909488 DOI: 10.3390/molecules24061150   
2019 Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S. Construction of a quadrangular tetramer and a cage-like hexamer from three-helix bundle-linked fusion proteins. Acs Synthetic Biology. PMID 30966743 DOI: 10.1021/acssynbio.9b00019   
2019 Dickerhoff J, Onel B, Chen L, Chen Y, Yang D. Solution Structure of a Promoter G-Quadruplex with 1:6:1 Loop Length. Acs Omega. 4: 2533-2539. PMID 30842981 DOI: 10.1021/acsomega.8b03580   
2019 Gulati S, Palczewski K, Engel A, Stahlberg H, Kovacik L. Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases. Science Advances. 5: eaav4322. PMID 30820458 DOI: 10.1126/sciadv.aav4322   
2019 Lee GR, Won J, Heo L, Seok C. GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure. Nucleic Acids Research. PMID 31001635 DOI: 10.1093/nar/gkz288   
2019 Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Plos Computational Biology. 15: e1006859. PMID 30917118 DOI: 10.1371/journal.pcbi.1006859   
2019 Shi L, Gao Z, Zhang T, Zhang H, Dong Y. Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens. Acta Crystallographica. Section F, Structural Biology Communications. 75: 153-158. PMID 30839288 DOI: 10.1107/S2053230X19000815   
2019 Schwartz M, Perrot T, Morel-Rouhier M, Mulliert G, Gelhaye E, Didierjean C, Favier F. The structure of Trametes versicolor Glutathione Transferase Omega 3S bound to its conjugation product GS-PEITC reveals plasticity of its active site. Protein Science : a Publication of the Protein Society. PMID 30972861 DOI: 10.1002/pro.3620   
2019 Inaba S, Shiota A, Yoshida T, Oda M. Protein structure and analysis site-specific observation of the conformational change of a protein with N-labeled Tyr residues using NMR. Analytical Biochemistry. PMID 30910701 DOI: 10.1016/j.ab.2019.03.009   
2019 Taechalertpaisarn J, Lyu RL, Arancillo M, Lin CM, Perez LM, Ioerger TR, Burgess K. Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis. Organic & Biomolecular Chemistry. PMID 30847453 DOI: 10.1039/c9ob00204a   
2019 Gerstman BS, Chapagain PP, Gc J, Steckmann T. Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins. Methods in Molecular Biology (Clifton, N.J.). 1958: 297-311. PMID 30945225 DOI: 10.1007/978-1-4939-9161-7_15   
2019 Ren W, Liu L, Gu L, Yan W, Feng Y, Dong D, Wang S, Wang C, Lyu M. Crystal structure of GH49 dextranase from Arthrobacter oxydans KQ11: the identification of catalytic base and the improvement of thermostability using semi-rational design based on B-factors. Journal of Agricultural and Food Chemistry. PMID 30919632 DOI: 10.1021/acs.jafc.9b01290   
2019 Rahman MM, Machuca MA, Roujeinikova A. Preliminary X-ray crystallographic studies on the Helicobacter pylori ABC transporter glutamine-binding protein GlnH. Drug Discoveries & Therapeutics. 13: 52-58. PMID 30880323 DOI: 10.5582/ddt.2019.01008   
2019 Cho HJ, Lee HJ, Cho HY, Park JW, Lee DS, Lee HS, Kwon OS, Kang BS. Structural basis for substrate binding to human pyridoxal 5'-phosphate phosphatase/chronophin by a conformational change. International Journal of Biological Macromolecules. PMID 30914363 DOI: 10.1016/j.ijbiomac.2019.03.097   
2019 Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sønderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcatili P. NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning. Proteins. PMID 30785653 DOI: 10.1002/prot.25674   
2019 Bansal A, Karanth NM, Demeler B, Schindelin H, Sarma SP. Crystallographic structures of IlvN●Val / Ile complexes: Conformational selectivity for feedback inhibition of AHASs. Biochemistry. PMID 30887800 DOI: 10.1021/acs.biochem.9b00050   
2019 Nair PC, McKinnon RA, Miners JO. Computational prediction of the site(s) of metabolism (SOM) and binding modes of protein kinase inhibitors metabolised by CYP3A4. Drug Metabolism and Disposition: the Biological Fate of Chemicals. PMID 30902802 DOI: 10.1124/dmd.118.085167   
2019 Wang W, Zhang Y, Wang L, Jing Q, Wang X, Xi X, Zhao X, Wang H. Molecular structure of thermostable and zinc-ion-binding γ-class carbonic anhydrases. Biometals : An International Journal On the Role of Metal Ions in Biology, Biochemistry, and Medicine. PMID 30895492 DOI: 10.1007/s10534-019-00190-8   
2019 Fischer T, Koulas SM, Tsagkarakou AS, Kyriakis E, Stravodimos GA, Skamnaki VT, Liggri PGV, Zographos SE, Riedl R, Leonidas DD. High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl--acyl-β-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors. Molecules (Basel, Switzerland). 24. PMID 30987252 DOI: 10.3390/molecules24071322   
2019 Koebke KJ, Pecoraro VL. Noncoded Amino Acids in de Novo Metalloprotein Design: Controlling Coordination Number and Catalysis. Accounts of Chemical Research. PMID 30933479 DOI: 10.1021/acs.accounts.9b00032   
2019 Sakuma M, Nishikawa S, Inaba S, Nishigaki T, Kojima S, Homma M, Imada K. Structure of the periplasmic domain of SflA involved in spatial regulation of the flagellar biogenesis of Vibrio reveals a TPR/SLR -like fold. Journal of Biochemistry. PMID 30989194 DOI: 10.1093/jb/mvz027   
2019 Shawki HH, Ishikawa-Yamauchi Y, Kawashima A, Katoh Y, Matsuda M, Al-Soudy AS, Minisy FM, Kuno A, Gulibaikelamu X, Hirokawa T, Takahashi S, Oishi H. EFCAB2 is a novel calcium-binding protein in mouse testis and sperm. Plos One. 14: e0214687. PMID 30933994 DOI: 10.1371/journal.pone.0214687   
2019 Dong J, Finn JA, Larsen PA, Smith TPL, Crowe JE. Structural Diversity of Ultralong CDRH3s in Seven Bovine Antibody Heavy Chains. Frontiers in Immunology. 10: 558. PMID 30967877 DOI: 10.3389/fimmu.2019.00558   
2019 Bari KJ, Sharma S, Chary KVR. Conformational dynamics study on human γS-crystallin as an efficient route to childhood blindness. Biochemical and Biophysical Research Communications. PMID 30827504 DOI: 10.1016/j.bbrc.2019.02.124   
2019 Russell RW, Fritz MP, Kraus J, Quinn CM, Polenova T, Gronenborn AM. Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'. Journal of Biomolecular Nmr. PMID 30847635 DOI: 10.1007/s10858-019-00233-9   
2019 Roccatano D, Hayward S. Free Energy Profile of Domain Movement in Ligand-Free Citrate Synthase. The Journal of Physical Chemistry. B. PMID 30744380 DOI: 10.1021/acs.jpcb.8b12001   
2019 Brown ZP, Takagi J. Advances in domain and subunit localization technology for electron microscopy. Biophysical Reviews. PMID 30834502 DOI: 10.1007/s12551-019-00513-6   
2019 Amir M, Kumar V, Dohare R, Rehman MT, Hussain A, Alajmi MF, El-Seedi HR, Hassan HMA, Islam A, Ahmad F, Hassan MI. Investigating architecture and structure-function relationships in cold shock DNA-binding domain family using structural genomics based approach. International Journal of Biological Macromolecules. PMID 31005689 DOI: 10.1016/j.ijbiomac.2019.04.135   
2019 Lee CW, Park SH, Koh HY, Jeong CS, Hwang J, Lee SG, Youn UJ, Lee CS, Park HH, Kim HJ, Park H, Lee JH. Crystal structure of a transcription factor, GerE (PaGerE), from spore-forming bacterium Paenisporosarcina sp. TG-14. Biochemical and Biophysical Research Communications. PMID 30967265 DOI: 10.1016/j.bbrc.2019.04.019   
2019 Stokes PH, Robertson NO, Silva AP, Estephan T, Trewhella J, Guss JM, Matthews JM. Mutation in a flexible linker modulates binding affinity for modular complexes. Proteins. PMID 30788856 DOI: 10.1002/prot.25675   
2019 Moretto L, Heylen R, Holroyd N, Vance S, Broadhurst RW. Modular type I polyketide synthase acyl carrier protein domains share a common N-terminally extended fold. Scientific Reports. 9: 2325. PMID 30787330 DOI: 10.1038/s41598-019-38747-9   
2019 Silva DR, Silla JM, Santos LA, da Cunha EFF, Freitas MP. The Role of Intramolecular Interactions on the Bioactive Conformation of Epinephrine. Molecular Informatics. PMID 30945816 DOI: 10.1002/minf.201800167   
2019 Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarné A. Binding of the regulatory domain of MutL to the sliding β-clamp is species specific. Nucleic Acids Research. PMID 30916336 DOI: 10.1093/nar/gkz115   
2019 Alex JM, Rennie ML, Engilberge S, Lehoczki G, Dorottya H, Fizil Á, Batta G, Crowley PB. Calixarene-mediated assembly of a small antifungal protein. Iucrj. 6: 238-247. PMID 30867921 DOI: 10.1107/S2052252519000411   
2019 Kwon S, Park HH. Crystal structure of the apo form of a β-transaminase from Mesorhizobium sp. strain LUK. Protein Science : a Publication of the Protein Society. PMID 30805955 DOI: 10.1002/pro.3594   
2019 Diener M, Adamcik J, Sanchez-Ferrer A, Jädig F, Schefer L, Mezzenga R. Primary, Secondary, Tertiary and Quaternary Structure Levels in Linear Polysaccharides - from Random Coil, to Single Helix to Supramolecular Assembly. Biomacromolecules. PMID 30816699 DOI: 10.1021/acs.biomac.9b00087   
2019 Birrane G, Dassier AL, Romashko A, Lundberg D, Holmes K, Cottle T, Norton AW, Zhang B, Concino MF, Meiyappan M. Structural characterization of the α-N-acetylglucosaminidase, a key enzyme in the pathogenesis of Sanfilippo syndrome B. Journal of Structural Biology. PMID 30802506 DOI: 10.1016/j.jsb.2019.02.005   
2019 Iwabuchi N, Maejima K, Kitazawa Y, Miyatake H, Nishikawa M, Tokuda R, Koinuma H, Miyazaki A, Nijo T, Oshima K, Yamaji Y, Namba S. Crystal structure of phyllogen, a phyllody-inducing effector protein of phytoplasma. Biochemical and Biophysical Research Communications. PMID 31010685 DOI: 10.1016/j.bbrc.2019.04.060