Dean R. Madden - Related publications

Biochemistry Dartmouth College, Hanover, NH, United States 
Biochemistry, General Biophysics, Microbiology Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Hallin EI, Bramham CR, Kursula P. Structural properties and peptide ligand binding of the capsid homology domains of human Arc. Biochemistry and Biophysics Reports. 26: 100975. PMID 33732907 DOI: 10.1016/j.bbrep.2021.100975   
2021 Le HT, Do PC, Le L. Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses. Evolutionary Bioinformatics Online. 17: 11769343211003082. PMID 33795930 DOI: 10.1177/11769343211003082   
2021 Weber F, Casalini T, Valentino G, Brülisauer L, Andreas N, Koeberle A, Kamradt T, Contini A, Luciani P. Targeting transdifferentiated hepatic stellate cells and monitoring the hepatic fibrogenic process by means of IGF2R-specific peptides designed . Journal of Materials Chemistry. B. PMID 33595041 DOI: 10.1039/d0tb02372h   
2021 Ploetz E, Schuurman-Wolters GK, Zijlstra N, Jager AW, Griffith DA, Guskov A, Gouridis G, Poolman B, Cordes T. Structural and biophysical characterization of the tandem substrate-binding domains of the ABC importer GlnPQ. Open Biology. 11: 200406. PMID 33823661 DOI: 10.1098/rsob.200406   
2021 Mohanty AK, Choudhary S, Kaushik JK, Fisher AJ. Crystal structure of BRP39, a signaling glycoprotein expressed during mammary gland apoptosis at 2.6 Å resolution. Journal of Structural Biology. 107737. PMID 33838225 DOI: 10.1016/j.jsb.2021.107737   
2021 Wang B, Su Z, Wu Y. Computational Assessment of Protein-Protein Binding Affinity by Reverse Engineering the Energetics in Protein Complexes. Genomics, Proteomics & Bioinformatics. PMID 33838354 DOI: 10.1016/j.gpb.2021.03.004   
2021 Kim TY, Cha JS, Kim H, Choi Y, Cho HS, Kim HS. Computationally-guided design and affinity improvement of a protein binder targeting a specific site on HER2. Computational and Structural Biotechnology Journal. 19: 1325-1334. PMID 33738081 DOI: 10.1016/j.csbj.2021.02.013   
2021 Bae JE, Kim IJ, Xu Y, Nam KH. Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus. The Protein Journal. PMID 33651244 DOI: 10.1007/s10930-021-09970-z   
2021 Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723038 DOI: 10.1073/pnas.2012800118   
2021 Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale quantum chemical computation of bio-molecular systems: the case of Spike protein of SARS-CoV-2 virus. Computational and Structural Biotechnology Journal. PMID 33623641 DOI: 10.1016/j.csbj.2021.02.004   
2021 Ortet PC, Muellers SN, Viarengo-Baker LA, Streu K, Szymczyna BR, Beeler AB, Allen KN, Whitty A. Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. Journal of the American Chemical Society. PMID 33683866 DOI: 10.1021/jacs.0c09799   
2021 Fischer TF, Schoeder CT, Zellmann T, Stichel J, Meiler J, Beck-Sickinger AG. Cyclic Analogues of the Chemerin C-Terminus Mimic a Loop Conformation Essential for Activating the Chemokine-like Receptor 1. Journal of Medicinal Chemistry. PMID 33705662 DOI: 10.1021/acs.jmedchem.0c01804   
2021 Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Acs Nano. PMID 33733740 DOI: 10.1021/acsnano.0c10833   
2021 Zhang S, Gong W, Han Z, Liu Y, Li C. Insight into Shared Properties and Differential Dynamics and Specificity of Secretory Phospholipase A Family Members. The Journal of Physical Chemistry. B. PMID 33780247 DOI: 10.1021/acs.jpcb.1c01315   
2021 Ludwig J, Smith J, Pfaendtner J. Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin. The Journal of Physical Chemistry. B. PMID 33715376 DOI: 10.1021/acs.jpcb.1c00221   
2021 Bock A, Bermudez M. Allosteric coupling and biased agonism in G protein-coupled receptors. The Febs Journal. PMID 33621418 DOI: 10.1111/febs.15783   
2021 Li H, Cao Z, Hu G, Zhao L, Wang C, Wang J. Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations. Technology and Health Care : Official Journal of the European Society For Engineering and Medicine. PMID 33682750 DOI: 10.3233/THC-218011   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Buchholz I, McDonnell T, Nestler P, Tharad S, Kulke M, Radziszewska A, Ripoll VM, Schmidt F, Hammer E, Toca-Herrera JL, Rahman A, Delcea M. Specific domain V reduction of beta-2-glycoprotein I induces protein flexibility and alters pathogenic antibody binding. Scientific Reports. 11: 4542. PMID 33633190 DOI: 10.1038/s41598-021-84021-2   
2021 Mizsei R, Li X, Chen WN, Szabo M, Wang JH, Wagner G, Reinherz EL, Mallis RJ. A general chemical crosslinking strategy for structural analyses of weakly interacting proteins applied to preTCR-pMHC complexes. The Journal of Biological Chemistry. 296: 100255. PMID 33837736 DOI: 10.1016/j.jbc.2021.100255   
2021 Stuffle EC, Johnson MS, Watts KJ. PAS domains in bacterial signal transduction. Current Opinion in Microbiology. 61: 8-15. PMID 33647528 DOI: 10.1016/j.mib.2021.01.004   
2021 Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. Journal of Molecular Modeling. 27: 106. PMID 33694107 DOI: 10.1007/s00894-021-04721-4   
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002   
2021 Ganotra GK, Nunes-Alves A, Wade RC. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time. Methods in Molecular Biology (Clifton, N.J.). 2266: 171-186. PMID 33759127 DOI: 10.1007/978-1-0716-1209-5_10   
2021 Karoyan P, Vieillard V, Gómez-Morales L, Odile E, Guihot A, Luyt CE, Denis A, Grondin P, Lequin O. Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection. Communications Biology. 4: 197. PMID 33580154 DOI: 10.1038/s42003-021-01736-8   
2021 You Y, Katti S, Yu B, Igumenova TI, Das J. Probing the Diacylglycerol Binding Site of Presynaptic Munc13-1. Biochemistry. PMID 33818064 DOI: 10.1021/acs.biochem.1c00165   
2021 Ma N, Nivedha AK, Vaidehi N. Allosteric Communication Regulates Ligand-Specific GPCR Activity. The Febs Journal. PMID 33738925 DOI: 10.1111/febs.15826   
2021 Lamers S, Feng Q, Cheng Y, Yu S, Sun B, Lukman M, Jiang J, Ruiz-Carrillo D. Structural and kinetic characterization of glutaminyl cyclase. Biological Chemistry. PMID 33823093 DOI: 10.1515/hsz-2020-0298   
2021 Ajadi MB, Soremekun OS, Elrashedy AA, Olotu FA, Kumalo HM, Soliman MES. Probing Protein-Protein Interactions and Druggable Site Identification: Mechanistic Binding Events between Ubiquitin and Zinc Finger with UFM1-Specific Peptidase Domain Protein (ZUFSP). Combinatorial Chemistry & High Throughput Screening. PMID 33538664 DOI: 10.2174/1386207324666210203175142   
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136   
2021 Weng YL, Naik SR, Dingelstad N, Lugo MR, Kalyaanamoorthy S, Ganesan A. Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity. Scientific Reports. 11: 7429. PMID 33795718 DOI: 10.1038/s41598-021-86471-0   
2021 Vuorio J, Škerlová J, Fábry M, Veverka V, Vattulainen I, Řezáčová P, Martinez-Seara H. N-Glycosylation can selectively block or foster different receptor-ligand binding modes. Scientific Reports. 11: 5239. PMID 33664400 DOI: 10.1038/s41598-021-84569-z   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 Talaia G, Amick J, Ferguson SM. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33597295 DOI: 10.1073/pnas.2014941118   
2021 Josephs TM, Belousoff MJ, Liang YL, Piper SJ, Cao J, Garama DJ, Leach K, Gregory KJ, Christopoulos A, Hay DL, Danev R, Wootten D, Sexton PM. Structure and dynamics of the CGRP receptor in apo and peptide-bound forms. Science (New York, N.Y.). PMID 33602864 DOI: 10.1126/science.abf7258   
2021 Freitas FC, Ferreira PHB, Favaro DC, Oliveira RJ. Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides. Journal of Chemical Information and Modeling. PMID 33619962 DOI: 10.1021/acs.jcim.0c01320   
2021 Jhaveri A, Maisuria D, Varga M, Mohammadyani D, Johnson ME. Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations. The Journal of Physical Chemistry. B. PMID 33826319 DOI: 10.1021/acs.jpcb.0c10992   
2021 Nešić D, Bush M, Spasic A, Li J, Kamata T, Handa M, Filizola M, Walz T, Coller BS. Electron microscopy shows that binding of monoclonal antibody PT25-2 primes integrin αIIbβ3 for ligand binding. Blood Advances. 5: 1781-1790. PMID 33760023 DOI: 10.1182/bloodadvances.2020004166   
2021 Zhang Y, Greer RA, Song Y, Praveen H, Song Y. In silico identification of available drugs targeting cell surface BiP to disrupt SARS-CoV-2 binding and replication: Drug repurposing approach. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 105771. PMID 33617948 DOI: 10.1016/j.ejps.2021.105771   
2021 Aljoundi A, El Rashedy A, Soliman MES. Distinguishing the optimal binding mechanism through reversible and irreversible inhibition analysis of HSP72 protein in cancer therapy. Computers in Biology and Medicine. 132: 104301. PMID 33751994 DOI: 10.1016/j.compbiomed.2021.104301   
2021 Shao G, Bao J, Pan X, He X, Qi Y, Zhang JZH. Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands. Frontiers in Molecular Biosciences. 8: 646524. PMID 33778009 DOI: 10.3389/fmolb.2021.646524   
2021 Escalante DE, Ferguson DM. Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2. Medicinal Chemistry Research : An International Journal For Rapid Communications On Design and Mechanisms of Action of Biologically Active Agents. 1-11. PMID 33564221 DOI: 10.1007/s00044-021-02708-7   
2021 Freidel MR, Armen RS. Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. Plos One. 16: e0246181. PMID 33596235 DOI: 10.1371/journal.pone.0246181   
2021 Park SS, Lee S, Rhee DK. Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain. Molecules and Cells. 44: 179-185. PMID 33795535 DOI: 10.14348/molcells.2021.2235   
2021 Knight KM, Ghosh S, Campbell SL, Lefevre TJ, Olsen RHJ, Smrcka AV, Valentin NH, Yin G, Vaidehi N, Dohlman HG. A universal allosteric mechanism for G protein activation. Molecular Cell. PMID 33636126 DOI: 10.1016/j.molcel.2021.02.002   
2021 Shi RL, Xiao G, Dillon TM, McAuley A, Ricci MS, Bondarenko PV. Identification of critical chemical modifications by size exclusion chromatography of stressed antibody-target complexes with competitive binding. Mabs. 13: 1887612. PMID 33616001 DOI: 10.1080/19420862.2021.1887612   
2021 Shang J, Kojetin DJ. Structural mechanism underlying ligand binding and activation of PPARγ. Structure (London, England : 1993). PMID 33713599 DOI: 10.1016/j.str.2021.02.006   
2021 Zheng W, Wen H. Predicting lipid and ligand binding sites in TRPV1 channel by molecular dynamics simulation and machine learning. Proteins. PMID 33739482 DOI: 10.1002/prot.26075   
2021 Kelly C, Pace N, Gage M, Pfuhl M. Solution NMR structure of titin N2A region Ig domain I83 and its interaction with metal ions. Journal of Molecular Biology. 166977. PMID 33811919 DOI: 10.1016/j.jmb.2021.166977   
2021 Williams-Noonan BJ, Todorova N, Kulkarni K, Aguilar MI, Yarovsky I. An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2. The Journal of Physical Chemistry. B. PMID 33657325 DOI: 10.1021/acs.jpcb.0c11321