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David R. Davies, Ph.D. - Related publications

NIDDK, NIH, Bethesda, MD, United States 
structural biology, crystallography, innate immune system
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W. The Induction Mechanism of the Flavonoid-Responsive Regulator FrrA. The Febs Journal. PMID 34314575 DOI: 10.1111/febs.16141   
2021 Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209   
2021 Kondra S, Chen F, Chen Y, Chen Y, Collette CJ, Xu W. A study of a hierarchical structure of proteins and ligand binding sites of receptors using the TSR-based structure comparison method and development of a size-filtering feature designed for comparing different sizes of protein structures. Proteins. PMID 34392570 DOI: 10.1002/prot.26215   
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W. Structures of heat shock factor trimers bound to DNA. Iscience. 24: 102951. PMID 34458700 DOI: 10.1016/j.isci.2021.102951   
2021 Park T, Woo H, Yang J, Kwon S, Won J, Seok C. Protein Oligomer Structure Prediction using GALAXY in CASP14. Proteins. PMID 34363243 DOI: 10.1002/prot.26203   
2021 Aggarwal R, Gupta A, Chelur V, Jawahar CV, Priyakumar UD. DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks. Journal of Chemical Information and Modeling. PMID 34374539 DOI: 10.1021/acs.jcim.1c00799   
2021 An X, Bai Q, Bing Z, Liu H, Yao X. Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations. Computational and Structural Biotechnology Journal. 19: 3978-3989. PMID 34377364 DOI: 10.1016/j.csbj.2021.07.008   
2021 Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallographica. Section D, Structural Biology. 77: 1099-1115. PMID 34342282 DOI: 10.1107/S2059798321006513   
2021 Toyama Y, Harkness RW, Kay LE. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446566 DOI: 10.1073/pnas.2111257118   
2021 Kumar A, Singh R, Ghosh B, Makde RD. Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly. Proteins. PMID 34431561 DOI: 10.1002/prot.26220   
2021 Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T, Nishimura C. Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability. Protein Science : a Publication of the Protein Society. PMID 34523753 DOI: 10.1002/pro.4184   
2021 Williams AN, Sherman MB, Smith HQ, Taube S, Pettitt BM, Wobus CE, Smith TJ. Multiple signals in the gut contract the mouse norovirus capsid to block antibody binding while enhancing receptor affinity. Journal of Virology. JVI0147121. PMID 34468172 DOI: 10.1128/JVI.01471-21   
2021 Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Research. PMID 34432045 DOI: 10.1093/nar/gkab736   
2021 Masuyer G, Davies JR, Stenmark P. Mechanism of Ganglioside Receptor Recognition by Botulinum Neurotoxin Serotype E. International Journal of Molecular Sciences. 22. PMID 34361086 DOI: 10.3390/ijms22158315   
2021 Cao H, Sun Y, Wang L, Pan Y, Li Z, Liang Y. In silico identification of novel inhibitors targeting the DNA-binding domain of the human estrogen receptor alpha. The Journal of Steroid Biochemistry and Molecular Biology. 105966. PMID 34416373 DOI: 10.1016/j.jsbmb.2021.105966   
2021 Chen EH, Lin KM, Sang JC, Ho MR, Lee CH, Shih O, Su CJ, Yeh YQ, Jeng US, Chen RP. Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein. Iubmb Life. PMID 34288372 DOI: 10.1002/iub.2528   
2021 Chen EH, Lin KM, Sang JC, Ho MR, Lee CH, Shih O, Su CJ, Yeh YQ, Jeng US, Chen RP. Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein. Iubmb Life. PMID 34288372 DOI: 10.1002/iub.2528   
2021 Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Communications Biology. 4: 916. PMID 34316015 DOI: 10.1038/s42003-021-02387-5   
2021 Wu P, Zhen X, Li B, Yu Q, Huang X, Shi N. Crystal structure of the MyRF ICA domain with its upstream β-helical stalk reveals the molecular mechanisms underlying its trimerization and self-cleavage. International Journal of Biological Sciences. 17: 2931-2943. PMID 34345217 DOI: 10.7150/ijbs.57673   
2021 Geerds C, Haas A, Niemann HH. Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB. Acta Crystallographica. Section F, Structural Biology Communications. 77: 246-253. PMID 34341190 DOI: 10.1107/S2053230X2100738X   
2021 Wang JC, Chen L. Structural basis for the structural dynamics of human mitochondrial chaperonin mHsp60. Scientific Reports. 11: 14809. PMID 34285302 DOI: 10.1038/s41598-021-94236-y   
2021 Abdollahi K, Condict L, Hung A, Kasapis S. Binding parameters and molecular dynamics of β-lactoglobulin-vanillic acid complexation as a function of pH - part B: Neutral pH. Food Chemistry. 367: 130655. PMID 34371277 DOI: 10.1016/j.foodchem.2021.130655   
2021 Tetreau G, Andreeva EA, Banneville AS, De Zitter E, Colletier JP. How Does Crystallize Such a Large Diversity of Toxins? Toxins. 13. PMID 34206796 DOI: 10.3390/toxins13070443   
2021 Abraham ET, Oecal S, Mörgelin M, Schmid PWN, Buchner J, Baumann U, Gebauer JM. Collagen's primary structure determines collagen:HSP47 complex stoichiometry. The Journal of Biological Chemistry. 101169. PMID 34487762 DOI: 10.1016/j.jbc.2021.101169   
2021 Jiang Z, Hu S, Ma J, Liu Y, Qiao Z, Yan Q, Gao Y, Yang S. Crystal structure of a chitinase (RmChiA) from the thermophilic fungus Rhizomucor miehei with a real active site tunnel. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140709. PMID 34358705 DOI: 10.1016/j.bbapap.2021.140709   
2021 Sahoo S, Dehury B, Narang PK, Raina V, Misra N, Suar M. Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an study to vitalize the development of optimum engineered strains with high lipid productivity. Journal of Biomolecular Structure & Dynamics. 1-19. PMID 34415234 DOI: 10.1080/07391102.2021.1967194   
2021 Gruschus JM, Yakovlev S, Banerjee K, Medved L, Tjandra N. Structural Basis for the Interaction of Fibrin with the Very Low-Density Lipoprotein Receptor Revealed by NMR and Site-Directed Mutagenesis. Biochemistry. PMID 34351135 DOI: 10.1021/acs.biochem.1c00378   
2021 Malliavin TE. Tandem domain structure determination based on a systematic enumeration of conformations. Scientific Reports. 11: 16925. PMID 34413388 DOI: 10.1038/s41598-021-96370-z   
2021 Turner LD, Nielsen AL, Lin L, Campedelli AJ, Silvaggi NR, Chen JS, Wakefield AE, Allen KN, Janda KD. Use of Crystallography and Molecular Modeling for the Inhibition of the Botulinum Neurotoxin A Protease. Acs Medicinal Chemistry Letters. 12: 1318-1324. PMID 34413962 DOI: 10.1021/acsmedchemlett.1c00325   
2021 Li Q, Kang C. Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines. 9. PMID 34440248 DOI: 10.3390/biomedicines9081044   
2021 Wallerstein J, Ekberg V, Ignjatović MM, Kumar R, Caldararu O, Peterson K, Wernersson S, Brath U, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. Jacs Au. 1: 484-500. PMID 34467311 DOI: 10.1021/jacsau.0c00094   
2021 Dash R, Mitra S, Munni YA, Choi HJ, Ali MC, Barua L, Jang TJ, Moon IS. Computational Insights into the Deleterious Impacts of Missense Variants on -Acetyl-d-glucosamine Kinase Structure and Function. International Journal of Molecular Sciences. 22. PMID 34360815 DOI: 10.3390/ijms22158048   
2021 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34475217 DOI: 10.1073/pnas.2106195118   
2021 Martins T, Meng Y, Korona B, Suckling R, Johnson S, Handford PA, Lea SM, Bray SJ. The conserved C2 phospholipid-binding domain in Delta contributes to robust Notch signalling. Embo Reports. e52729. PMID 34347930 DOI: 10.15252/embr.202152729   
2021 T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. The Journal of Physical Chemistry. B. PMID 34423989 DOI: 10.1021/acs.jpcb.1c01227   
2021 Bibbe JM, Vriend G. Motions around conserved helical weak spots facilitate GPCR activation. Proteins. PMID 34272892 DOI: 10.1002/prot.26179   
2021 Sobti M, Ueno H, Noji H, Stewart AG. The six steps of the complete F-ATPase rotary catalytic cycle. Nature Communications. 12: 4690. PMID 34344897 DOI: 10.1038/s41467-021-25029-0   
2021 Chen J, White A, Nelson DC, Shukla D. Role of substrate recognition in modulating strigolactone receptor selectivity in witchweed. The Journal of Biological Chemistry. 101092. PMID 34437903 DOI: 10.1016/j.jbc.2021.101092   
2021 Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallographica. Section D, Structural Biology. 77: 1168-1182. PMID 34473087 DOI: 10.1107/S2059798321008196   
2021 Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. Plos One. 16: e0257206. PMID 34506566 DOI: 10.1371/journal.pone.0257206   
2021 Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Characterization of a A3G-Vif-CRL5-CBFβ structure using a cross-linking mass spectrometry pipeline for integrative modeling of host-pathogen complexes. Molecular & Cellular Proteomics : McP. 100132. PMID 34389466 DOI: 10.1016/j.mcpro.2021.100132   
2021 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188   
2021 Wang W, Liu Q, Liu Q, Hendrickson WA. Conformational equilibria in allosteric control of Hsp70 chaperones. Molecular Cell. PMID 34453889 DOI: 10.1016/j.molcel.2021.07.039   
2021 Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure (London, England : 1993). PMID 34331857 DOI: 10.1016/j.str.2021.07.001   
2021 Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods in Enzymology. 656: 1-25. PMID 34325784 DOI: 10.1016/bs.mie.2021.04.007   
2021 Ferreira GM, Kronenberger T, Tonduru AK, Hirata RDC, Hirata MH, Poso A. SARS-COV-2 M conformational changes induced by covalently bound ligands. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 34516349 DOI: 10.1080/07391102.2021.1970626   
2021 Bie LH, Fei JW, Gao J. Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer. Journal of Molecular Modeling. 27: 227. PMID 34264385 DOI: 10.1007/s00894-021-04840-y   
2021 Cao Y, Choi YK, Frank M, Woo H, Park SJ, Yeom MS, Seok C, Im W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. Journal of Chemical Theory and Computation. PMID 34529436 DOI: 10.1021/acs.jctc.1c00552   
2021 Ali MS, Rehman MT, Al-Lohedan HA, AlAjmi MF. Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods. Journal of Biomolecular Structure & Dynamics. 1-9. PMID 34488560 DOI: 10.1080/07391102.2021.1971560