Ruben Diaz-Avalos, Ph.D. - Related publications

HHMI Janelia Farm Research Campus, Ashburn, VA, United States 
Structural Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Jia Z, Liu C, Chen Y, Jiang H, Wang Z, Yao J, Yang J, Zhu J, Zhang B, Yuchi Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. The Febs Journal. PMID 34665939 DOI: 10.1111/febs.16239   
2021 Oliveira NFB, Rodrigues FEP, Vitorino JNM, Loureiro RJS, Faísca PFN, Machuqueiro M. Predicting stable binding modes from simulated dimers of the D76N mutant of 2-microglobulin. Computational and Structural Biotechnology Journal. 19: 5160-5169. PMID 34630936 DOI: 10.1016/j.csbj.2021.09.003   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Webby MN, Herr N, Bulloch EMM, Schmitz M, Keown JR, Goldstone DC, Kingston RL. Structural Analysis of the Menangle Virus P Protein Reveals a Soft Boundary between Ordered and Disordered Regions. Viruses. 13. PMID 34578318 DOI: 10.3390/v13091737   
2021 Catalano C, Al Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Current Research in Structural Biology. 3: 239-256. PMID 34693344 DOI: 10.1016/j.crstbi.2021.09.002   
2021 Gouridis G, Muthahari YA, de Boer M, Griffith DA, Tsirigotaki A, Tassis K, Zijlstra N, Xu R, Eleftheriadis N, Sugijo Y, Zacharias M, Dömling A, Karamanou S, Pozidis C, Economou A, et al. Structural dynamics in the evolution of a bilobed protein scaffold. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34845009 DOI: 10.1073/pnas.2026165118   
2021 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Collu G, Bierig T, Krebs AS, Engilberge S, Varma N, Guixà-González R, Sharpe T, Deupi X, Olieric V, Poghosyan E, Benoit RM. Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology. Structure (London, England : 1993). PMID 34587504 DOI: 10.1016/j.str.2021.09.002   
2021 Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Communications Biology. 4: 1240. PMID 34716407 DOI: 10.1038/s42003-021-02766-y   
2021 Kumar A, Kumar P, Saumya KU, Giri R. Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microbial Pathogenesis. 161: 105236. PMID 34648928 DOI: 10.1016/j.micpath.2021.105236   
2021 Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. Journal of the American Chemical Society. PMID 34757725 DOI: 10.1021/jacs.1c10588   
2021 Basha SJ, Rao KY, Monika K, Gajula NN, Dubey S, Reddy ABM, Subramanyam R, Damu AG. Deciphering the AChE-binding mechanism with multifunctional tricyclic coumarin anti-Alzheimer's agents using biophysical and bioinformatics approaches and evaluation of their modulating effect on Amyloidogenic peptide assembly. International Journal of Biological Macromolecules. PMID 34740688 DOI: 10.1016/j.ijbiomac.2021.10.204   
2021 Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochemical and Biophysical Research Communications. 583: 43-48. PMID 34735878 DOI: 10.1016/j.bbrc.2021.10.051   
2021 Lee SY, Kwon S, Ha HJ, Lee SH, Park HH. Helical filament structure of the DREP3 CIDE domain reveals a unified mechanism of CIDE-domain assembly. Acta Crystallographica. Section D, Structural Biology. 77: 1543-1553. PMID 34866610 DOI: 10.1107/S2059798321010767   
2021 Zhang C, Li Y, Samad A, Zheng P, Ji Z, Chen F, Zhang H, Jin T. Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY. International Journal of Biological Macromolecules. PMID 34856215 DOI: 10.1016/j.ijbiomac.2021.11.129   
2021 Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj. 8: 954-962. PMID 34804547 DOI: 10.1107/S2052252521009386   
2021 Poelman H, Ippel H, Gürkan B, Boelens R, Vriend G, Veer CV', Lutgens E, Nicolaes GAF. Structural anomalies in a published NMR-derived structure of IRAK-M. Journal of Molecular Graphics & Modelling. 111: 108061. PMID 34837785 DOI: 10.1016/j.jmgm.2021.108061   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Minato T, Teramoto T, Adachi N, Hung NK, Yamada K, Kawasaki M, Akutsu M, Moriya T, Senda T, Ogo S, Kakuta Y, Yoon KS. Non-conventional octameric structure of C-phycocyanin. Communications Biology. 4: 1238. PMID 34716405 DOI: 10.1038/s42003-021-02767-x   
2021 Liu W, Chen J, Jin L, Liu ZY, Lu M, Jiang G, Yang Q, Quan C, Nam KH, Xu Y. Functional and structural analysis of catabolite control protein C that responds to citrate. Scientific Reports. 11: 20285. PMID 34645869 DOI: 10.1038/s41598-021-99552-x   
2021 Dawson WM, Martin FJO, Rhys GG, Shelley KL, Brady RL, Woolfson DN. Coiled coils 9-to-5: rational design of α-helical barrels with tunable oligomeric states. Chemical Science. 12: 6923-6928. PMID 34745518 DOI: 10.1039/d1sc00460c   
2021 James JK, Nanda V. A Folding Insulator Defines Cryptic Domains in Tropomyosin. Journal of Molecular Biology. 433: 167281. PMID 34606830 DOI: 10.1016/j.jmb.2021.167281   
2021 Soltanikazemi E, Quadir F, Roy RS, Guo Z, Cheng J. Distance-based Reconstruction of Protein Quaternary Structures from Inter-Chain Contacts. Proteins. PMID 34716620 DOI: 10.1002/prot.26269   
2021 Morand J, Nunes A, Faísca PFN. The folding space of protein2-microglobulin is modulated by a single disulfide bridge. Physical Biology. 18. PMID 34098544 DOI: 10.1088/1478-3975/ac08ec   
2021 Yang W, Kim BS, Muniyappan S, Lee YH, Kim JH, Yu W. Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift. Frontiers in Molecular Biosciences. 8: 766830. PMID 34746240 DOI: 10.3389/fmolb.2021.766830   
2021 Jang H, Lee C, Hwang Y, Lee SJ. Concanavalin A: coordination diversity to xenobiotic metal ions and biological consequences. Dalton Transactions (Cambridge, England : 2003). PMID 34806716 DOI: 10.1039/d1dt03501k   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Ramírez CS, Tolmie C, Opperman DJ, González PJ, Rivas MG, Brondino CD, Ferroni FM. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator. Protein Science : a Publication of the Protein Society. 30: 2310-2323. PMID 34562300 DOI: 10.1002/pro.4195   
2021 Mishra RP, Goel G. Multiscale Model for Quantitative Prediction of Insulin Aggregation Nucleation Kinetics. Journal of Chemical Theory and Computation. PMID 34813303 DOI: 10.1021/acs.jctc.1c00499   
2021 Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. The Journal of Physical Chemistry. B. PMID 34748336 DOI: 10.1021/acs.jpcb.1c05820   
2021 Chandonia JM, Guan L, Lin S, Yu C, Fox NK, Brenner SE. SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. Nucleic Acids Research. PMID 34850923 DOI: 10.1093/nar/gkab1054   
2021 Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, et al. Structure, function and pharmacology of human itch receptor complexes. Nature. PMID 34789875 DOI: 10.1038/s41586-021-04077-y   
2021 Shiratori T, Goto S, Sakaguchi T, Kasai T, Otsuka Y, Higashi K, Makino K, Takahashi H, Komatsu K. Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins. Biochemistry and Biophysics Reports. 28: 101153. PMID 34712848 DOI: 10.1016/j.bbrep.2021.101153   
2021 Cui H, Müller AU, Leibundgut M, Tian J, Ban N, Weber-Ban E. Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Nature Communications. 12: 6635. PMID 34789727 DOI: 10.1038/s41467-021-26848-x   
2021 Juanes-Gusano D, Santos M, Reboto V, Alonso M, Rodríguez-Cabello JC. Self-assembling systems comprising intrinsically disordered protein polymers like elastin-like recombinamers. Journal of Peptide Science : An Official Publication of the European Peptide Society. e3362. PMID 34545666 DOI: 10.1002/psc.3362   
2021 Martínez-Caballero S, Mahasenan KV, Kim C, Molina R, Feltzer R, Lee M, Bouley R, Hesek D, Fisher JF, Muñoz IG, Chang M, Mobashery S, Hermoso JA. Integrative structural biology of the penicillin-binding protein-1 from , an essential component of the divisome machinery. Computational and Structural Biotechnology Journal. 19: 5392-5405. PMID 34667534 DOI: 10.1016/j.csbj.2021.09.018   
2021 Zhao Q, Yuan JJ, Hu F, Qian C, Tian CF, Wang JT, Gao D, Yi W, Wang HB. Isolation, physicochemical, and structure-function relationship of the hydrophobic variant of Fc-fusion proteins that bind to TNF-α receptor, HS002 and HS002A. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1186: 123026. PMID 34781108 DOI: 10.1016/j.jchromb.2021.123026   
2021 Saporiti S, Parravicini C, Pergola C, Guerrini U, Rossi M, Centola F, Eberini I. IgG1 conformational behavior: elucidation of the N-glycosylation role via molecular dynamics. Biophysical Journal. PMID 34710380 DOI: 10.1016/j.bpj.2021.10.026   
2021 Xu YC, ShangGuan TJ, Ding XM, Cheung NJ. Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network. Scientific Reports. 11: 21033. PMID 34702851 DOI: 10.1038/s41598-021-00477-2   
2021 Yu X, Mullen TM, Abrishami V, Huiskonen JT, Nemerow GR, Reddy VS. Structure of a cell entry defective human adenovirus provides insights into precursor proteins and capsid maturation. Journal of Molecular Biology. 167350. PMID 34774568 DOI: 10.1016/j.jmb.2021.167350   
2021 Manoilov KY, Ghosh A, Almo SC, Verkhusha VV. Structural and Functional Characterization of a Biliverdin-Binding Near-Infrared Fluorescent Protein From the Serpin Superfamily. Journal of Molecular Biology. 434: 167359. PMID 34798132 DOI: 10.1016/j.jmb.2021.167359   
2021 Hu A, Zhao Q, Chen L, Zhao J, Wang Y, Feng K, Wu L, Xie M, Zhou X, Xiao L, Ming Z, Zhang M, Yao R. Identification of Conserved and Divergent Strigolactone Receptors in Sugarcane Reveals a Key Residue Crucial for Plant Branching Control. Frontiers in Plant Science. 12: 747160. PMID 34858455 DOI: 10.3389/fpls.2021.747160   
2021 Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov AV, Elghobashi-Meinhardt N, Wells G, Harris SA, Frezza E, Rosta E. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chemical Science. 12: 13492-13505. PMID 34777769 DOI: 10.1039/d1sc02775a   
2021 Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, et al. Structure of cytochrome in complex with Q203 and TB47, two anti-TB drug candidates. Elife. 10. PMID 34819223 DOI: 10.7554/eLife.69418   
2021 Liu X, Yang S, Hart JR, Xu Y, Zou X, Zhang H, Zhou Q, Xia T, Zhang Y, Yang D, Wang MW, Vogt PK. Cryo-EM structures of PI3Kα reveal conformational changes during inhibition and activation. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34725156 DOI: 10.1073/pnas.2109327118   
2021 Ho TNT, Lee HS, Swaminathan S, Goodwin L, Rai N, Ushay B, Lewis RJ, Rosengren KJ, Conibear AC. Posttranslational modifications of α-conotoxins: sulfotyrosine and C-terminal amidation stabilise structures and increase acetylcholine receptor binding. Rsc Medicinal Chemistry. 12: 1574-1584. PMID 34671739 DOI: 10.1039/d1md00182e   
2021 Kim DG, Baek I, Lee Y, Kim H, Kim JY, Bang G, Kim S, Yoon HJ, Han BW, Suh SW, Kim HS. Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins. Acta Crystallographica. Section D, Structural Biology. 77: 1460-1474. PMID 34726173 DOI: 10.1107/S2059798321010068   
2021 Stilianoudakis SC, Marshall MA, Dozmorov MG. preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution. Bioinformatics (Oxford, England). PMID 34741515 DOI: 10.1093/bioinformatics/btab743   
2021 Schulze-Niemand E, Naumann M, Stein M. Substrate-Assisted Activation and Selectivity of the Bacterial RavD Effector Deubiquitinylase. Proteins. PMID 34825414 DOI: 10.1002/prot.26286   
2021 Pal S, Bose D, Chakrabarti A, Chattopadhyay A. Comparative Analysis of Tryptophan Dynamics in Spectrin and Its Constituent Domains: Insights from Fluorescence. The Journal of Physical Chemistry. B. PMID 34845910 DOI: 10.1021/acs.jpcb.1c08600