Bryan D. Cox, Ph.D. - Related publications

Affiliations: 
2012 Chemistry University of Alabama, Birmingham, Birmingham, AL, United States 
Area:
Physical Chemistry, Biochemistry, General Biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Chen B, Fountain G, Sullivan HJ, Paradis N, Wu C. To probe the binding pathway of a selective compound (D089-0563) to c-MYC Pu24 G-quadruplex using free ligand binding simulations and Markov state model analysis. Physical Chemistry Chemical Physics : Pccp. PMID 33000836 DOI: 10.1039/d0cp03863f   
2020 Gavira JA, Matilla MA, Fernández M, Krell T. The structural basis for signal promiscuity in a bacterial chemoreceptor. The Febs Journal. PMID 33021055 DOI: 10.1111/febs.15580   
2020 Terrado M, Okon M, McIntosh LP, Plettner E. Ligand- and pH-Induced Structural Transition of Gypsy Moth Pheromone-Binding Protein 1 (LdisPBP1). Biochemistry. PMID 32877603 DOI: 10.1021/acs.biochem.0c00592   
2020 Patel K, Walport LJ, Walshe JL, Solomon PD, Low JKK, Tran DH, Mouradian KS, Silva APG, Wilkinson-White L, Norman A, Franck C, Matthews JM, Guss JM, Payne RJ, Passioura T, et al. Cyclic peptides can engage a single binding pocket through highly divergent modes. Proceedings of the National Academy of Sciences of the United States of America. PMID 33046654 DOI: 10.1073/pnas.2003086117   
2020 Liu Q, He QT, Lyu X, Yang F, Zhu ZL, Xiao P, Yang Z, Zhang F, Yang ZY, Wang XY, Sun P, Wang QW, Qu CX, Gong Z, Lin JY, et al. DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl H-NMR probe. Nature Communications. 11: 4857. PMID 32978402 DOI: 10.1038/s41467-020-18433-5   
2020 Churcher ZR, Garaev D, Hunter HN, Johnson PE. Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer. Biophysical Journal. PMID 32882188 DOI: 10.1016/j.bpj.2020.08.012   
2020 Pandey P, Prasad K, Prakash A, Kumar V. Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis. Journal of Molecular Medicine (Berlin, Germany). PMID 32965508 DOI: 10.1007/s00109-020-01980-1   
2020 Wang X, Bie L, Fei J, Gao J. Insights into the Loop at E-selectin Binding Site: from Open to Close Conformation. Journal of Chemical Information and Modeling. PMID 32941021 DOI: 10.1021/acs.jcim.0c00939   
2020 Sarfaraz S, Muneer I, Liu H. Combining fragment docking with graph theory to improve ligand docking for homology model structures. Journal of Computer-Aided Molecular Design. PMID 33034007 DOI: 10.1007/s10822-020-00345-7   
2020 Boulton S, Van K, VanSchouwen B, Augustine J, Akimoto M, Melacini G. Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding. Biophysical Journal. PMID 32882185 DOI: 10.1016/j.bpj.2020.07.038   
2020 Yan W, Cheng L, Wang W, Wu C, Yang X, Du X, Ma L, Qi S, Wei Y, Lu Z, Yang S, Shao Z. Structure of the human gonadotropin-releasing hormone receptor GnRH1R reveals an unusual ligand binding mode. Nature Communications. 11: 5287. PMID 33082324 DOI: 10.1038/s41467-020-19109-w   
2020 Katoh T, Sengoku T, Hirata K, Ogata K, Suga H. Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic β-amino acids. Nature Chemistry. PMID 32839601 DOI: 10.1038/s41557-020-0525-1   
2020 C S, S DK, Ragunathan V, Tiwari P, A S, P BD. Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. Journal of Biomolecular Structure & Dynamics. 1-27. PMID 32897178 DOI: 10.1080/07391102.2020.1815584   
2020 Basak S, Kumar A, Ramsey S, Gibbs E, Kapoor A, Filizola M, Chakrapani S. High-resolution structures of multiple 5-HTR-setron complexes reveal a novel mechanism of competitive inhibition. Elife. 9. PMID 33063666 DOI: 10.7554/eLife.57870   
2020 Harkness RW, Toyama Y, Kay LE. Analyzing multi-step ligand binding reactions for oligomeric proteins by NMR: Theoretical and computational considerations. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 318: 106802. PMID 32818875 DOI: 10.1016/j.jmr.2020.106802   
2020 Taidi L, Maurady A, Britel MR. Molecular docking study and molecular dynamic simulation of human cyclooxygenase-2 (COX-2) with selected eutypoids. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 32990169 DOI: 10.1080/07391102.2020.1823884   
2020 Gangwar SP, Green MN, Michard E, Simon AA, Feijó JA, Sobolevsky AI. Structure of the Arabidopsis Glutamate Receptor-like Channel GLR3.2 Ligand-Binding Domain. Structure (London, England : 1993). PMID 33027636 DOI: 10.1016/j.str.2020.09.006   
2020 Conrad M, Söldner CA, Miao Y, Sticht H. Agonist Binding and G Protein Coupling in Histamine H Receptor: A Molecular Dynamics Study. International Journal of Molecular Sciences. 21. PMID 32932742 DOI: 10.3390/ijms21186693   
2020 Cramer DL, Cheng B, Tian J, Clements JH, Wypych RM, Martin SF. Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions. European Journal of Medicinal Chemistry. 208: 112771. PMID 32916312 DOI: 10.1016/j.ejmech.2020.112771   
2020 Lv M, Gao J, Li M, Ma R, Li F, Liu Y, Liu M, Zhang J, Yao X, Wu J, Shi Y, Tang Y, Pan Y, Zhang ZY, Ruan K. Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. The Journal of Physical Chemistry Letters. PMID 32885980 DOI: 10.1021/acs.jpclett.0c02039   
2020 Mi T, Burgess K. Striking Similarities between CDRs in Some mAbs That Neutralize COVID-19. Acs Medicinal Chemistry Letters. 11: 1663-1666. PMID 32934769 DOI: 10.1021/acsmedchemlett.0c00409   
2020 Bozovic O, Zanobini C, Gulzar A, Jankovic B, Buhrke D, Post M, Wolf S, Stock G, Hamm P. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proceedings of the National Academy of Sciences of the United States of America. PMID 33020277 DOI: 10.1073/pnas.2012999117   
2020 Goba I, Goricanec D, Schum D, Hillenbrand M, Plückthun A, Hagn F. Probing the Conformational States of Neurotensin Receptor 1 Variants by NMR Site-Directed Methyl Labeling. Chembiochem : a European Journal of Chemical Biology. PMID 32881260 DOI: 10.1002/cbic.202000541   
2020 Sakamoto K, Hayashi A, Haruna KI, Sato H, Ito K, Makino C, Ito T. Incorporation of halogenated amino acids into antibody fragments at multiple specific sites enhances antigen binding. Chembiochem : a European Journal of Chemical Biology. PMID 32815262 DOI: 10.1002/cbic.202000429   
2020 Jaladanki CK, He Y, Zhao LN, Maurer-Stroh S, Loo LH, Song H, Fan H. Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids. Archives of Toxicology. PMID 32909075 DOI: 10.1007/s00204-020-02897-x   
2020 Chowdhury SM, Hossain MN, Rafe MR. design and evaluation of novel 5-fluorouracil analogues as potential anticancer agents. Heliyon. 6: e04978. PMID 33033767 DOI: 10.1016/j.heliyon.2020.e04978   
2020 Denisov SS, Ramírez-Escudero M, Heinzmann ACA, Ippel JH, Dawson PE, Koenen RR, Hackeng TM, Janssen BJC, Dijkgraaf I. Structural characterization of anti-CCL5 activity of the tick salivary protein Evasin-4. The Journal of Biological Chemistry. PMID 32817341 DOI: 10.1074/jbc.RA120.013891   
2020 Lokareddy RK, Ko YH, Hong N, Doll SG, Paduch M, Niederweis M, Kossiakoff AA, Cingolani G. Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment. Acta Crystallographica. Section D, Structural Biology. 76: 876-888. PMID 32876063 DOI: 10.1107/S2059798320009912   
2020 Yeldell SB, Seitz O. Nucleic acid constructs for the interrogation of multivalent protein interactions. Chemical Society Reviews. PMID 32870222 DOI: 10.1039/d0cs00518e   
2020 Lee HS, Wang SH, Daniel JT, Hossain MA, Clark RJ, Bathgate RAD, Rosengren KJ. Exploring the Use of Helicogenic Amino Acids for Optimising Single Chain Relaxin-3 Peptide Agonists. Biomedicines. 8. PMID 33066369 DOI: 10.3390/biomedicines8100415   
2020 Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A. Retrieving functional pathways of biomolecules from single-particle snapshots. Nature Communications. 11: 4734. PMID 32948759 DOI: 10.1038/s41467-020-18403-x   
2020 Nagarajan SK, Babu S, Sohn H, Madhavan T. Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)-Ligand Binding: A Structural Biology Study Based on Computational Methods. Acs Omega. 5: 21145-21161. PMID 32875251 DOI: 10.1021/acsomega.0c02847   
2020 Gulsevin A, Meiler J, Horenstein NA. A Computational Analysis of the Factors Governing the Dynamics of α7 nAChR and Its Homologs. Biophysical Journal. PMID 33010233 DOI: 10.1016/j.bpj.2020.09.006   
2020 Lima AM, Siqueira AS, Möller MLS, Souza RC, Cruz JN, Lima ARJ, Silva RCD, Aguiar DCF, Junior JLDSGV, Gonçalves EC. improvement of the cyanobacterial lectin microvirin and mannose interaction. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 32990187 DOI: 10.1080/07391102.2020.1821782   
2020 Aljoundi A, El Rashedy A, Appiah-Kubi P, Soliman MES. Coupling of HSP72 α-Helix Subdomains by the Unexpected Irreversible Targeting of Lysine-56 over Cysteine-17; Coevolution of Covalent Bonding. Molecules (Basel, Switzerland). 25. PMID 32947765 DOI: 10.3390/molecules25184239   
2020 Forouzesh N, Onufriev AV. MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor. Biorxiv : the Preprint Server For Biology. PMID 32869029 DOI: 10.1101/2020.08.25.267625   
2020 Zheng Y, Su J, Miller MC, Geng J, Xu X, Zhang T, Mayzel M, Zhou Y, Mayo KH, Tai G. Topsy-turvy binding of negatively charged homogalacturonan oligosaccharides to galectin-3. Glycobiology. PMID 32909036 DOI: 10.1093/glycob/cwaa080   
2020 Chandna R, Kaczanowska K, Taylor P, Kini RM. Drysdalin, a snake neurotoxin with higher affinity for soluble acetylcholine binding protein from Aplysia californica than from Lymnaea stagnalis. Toxicon : Official Journal of the International Society On Toxinology. 187: 86-92. PMID 32889025 DOI: 10.1016/j.toxicon.2020.08.030   
2020 Bochel AJ, Williams C, McCoy AJ, Hoppe HJ, Winter AJ, Nicholls RD, Harlos K, Jones EY, Berger I, Hassan AB, Crump MP. Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9. Structure (London, England : 1993). PMID 32877646 DOI: 10.1016/j.str.2020.08.002   
2020 Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science (New York, N.Y.). PMID 32907861 DOI: 10.1126/science.abd9909   
2020 Patel CN, Kumar SP, Pandya HA, Rawal RM. Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation. Molecular Diversity. PMID 32996011 DOI: 10.1007/s11030-020-10135-w   
2020 Shekhar N, Sarma P, Prajapat M, Avti P, Kaur H, Raja A, Singh H, Bhattacharya A, Sharma S, Kumar S, Prakash A, Medhi B. Structure-Based Repositioning of Approved Drugs for Spike Glycoprotein S2 Domain Fusion Peptide of SARS-CoV-2: Rationale from Molecular Dynamics and Binding Free Energy Calculations. Msystems. 5. PMID 32963099 DOI: 10.1128/mSystems.00382-20   
2020 Olson LJ, Misra SK, Ishihara M, Battaile KP, Grant OC, Sood A, Woods RJ, Kim JP, Tiemeyer M, Ren G, Sharp JS, Dahms NM. Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor. Communications Biology. 3: 498. PMID 32908216 DOI: 10.1038/s42003-020-01211-w   
2020 Fukuhara S, Kobayashi K, Kusakizako T, Iida W, Kato M, Shihoya W, Nureki O. Structure of the human secretin receptor coupled to an engineered heterotrimeric G protein. Biochemical and Biophysical Research Communications. PMID 33008599 DOI: 10.1016/j.bbrc.2020.08.042   
2020 Yamamoto K, Hiromori Y, Matsumaru D, Ishii Y, Takeshita Y, Tsubakihara I, Kimura T, Nagase H, Nakanishi T. Tri-substituted organotin compounds, but not retinoic acid, are potent ligands of complement component 8 γ. The Journal of Toxicological Sciences. 45: 581-587. PMID 32879257 DOI: 10.2131/jts.45.581   
2020 Ramanathan A, Parvatikar A, Chennubhotla SC, Mei Y, Sinha SC. Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain. Biomolecules. 10. PMID 32932757 DOI: 10.3390/biom10091308   
2020 Stadelmann T, Subramanian G, Menon S, Townsend CE, Lokey RS, Ebert MO, Riniker S. Connecting the conformational behavior of cyclic octadepsipeptides with their ionophoric property and membrane permeability. Organic & Biomolecular Chemistry. PMID 32902550 DOI: 10.1039/d0ob01447h   
2020 Jia J, Zhang L, Song J, Dai J, Cui M. Discovery of Diphenoxy Derivatives with Flexible Linkers as Ligands for β-amyloid Plaques. Molecular Pharmaceutics. PMID 32845647 DOI: 10.1021/acs.molpharmaceut.0c00537   
2020 Jamalpure S, Panditrao G, Kulabhusan PK, Hameed ASS, Paknikar KM, Joshi M, Rajwade JM. In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus. Journal of Molecular Modeling. 26: 264. PMID 32914310 DOI: 10.1007/s00894-020-04524-z   
2020 Liu J, Chen WM, Shao YH, Liu YP, Tu ZC. Improved antitumor activity and IgE/IgG-binding ability of α-Lactalbumin/β-lactoglobulin induced by ultrasonication prior to binding with oleic acid. Journal of Food Biochemistry. e13502. PMID 33025647 DOI: 10.1111/jfbc.13502