Joseph M. Simard, Ph.D. - Related publications

2007 Chemistry University of Massachusetts, Amherst, Amherst, MA 
Supramolecular Chemistry, Nanotechnology
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Walkowiak JJ, Ballauff M, Zimmermann R, Freudenberg U, Werner C. Thermodynamic Analysis of the Interaction of Heparin with Lysozyme. Biomacromolecules. PMID 32662630 DOI: 10.1021/acs.biomac.0c00780   
2020 Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. Journal of Medicinal Chemistry. PMID 33017535 DOI: 10.1021/acs.jmedchem.0c01500   
2020 Lucas JE, Kortemme T. New computational protein design methods for de novo small molecule binding sites. Plos Computational Biology. 16: e1008178. PMID 33017412 DOI: 10.1371/journal.pcbi.1008178   
2020 Santoro AM, D'Urso A, Cunsolo A, Milardi D, Purrello R, Sbardella D, Tundo GR, Diana D, Fattorusso R, Dato AD, Paladino A, Persico M, Coletta M, Fattorusso C. Cooperative Binding of the Cationic Porphyrin Tris-T4 Enhances Catalytic Activity of 20S Proteasome Unveiling a Complex Distribution of Functional States. International Journal of Molecular Sciences. 21. PMID 33003385 DOI: 10.3390/ijms21197190   
2020 Neira JL, Rizzuti B, Jiménez-Alesanco A, Abián O, Velázquez-Campoy A, Iovanna JL. The Paralogue of the Intrinsically Disordered Nuclear Protein 1 Has a Nuclear Localization Sequence that Binds to Human Importin α3. International Journal of Molecular Sciences. 21. PMID 33050086 DOI: 10.3390/ijms21197428   
2020 Danielsen MB, Christensen NJ, Jørgensen PT, Jensen KJ, Wengel J, Lou C. Polyamine-functionalized 2'-amino-LNA in oligonucleotides: Facile synthesis of novel monomers and high affinity binding towards ssDNA and dsDNA. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33073896 DOI: 10.1002/chem.202004495   
2020 Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, et al. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. Science Advances. 6. PMID 33148639 DOI: 10.1126/sciadv.abb5924   
2020 Henley MJ, Linhares BM, Morgan BS, Cierpicki T, Fierke CA, Mapp AK. Unexpected specificity within dynamic transcriptional protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. PMID 33077600 DOI: 10.1073/pnas.2013244117   
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   
2020 Yao X, Chen C, Wang Y, Dong S, Liu YJ, Li Y, Cui Z, Gong W, Perrett S, Yao L, Lamed R, Bayer EA, Cui Q, Feng Y. Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules. Science Advances. 6. PMID 33097546 DOI: 10.1126/sciadv.abd7182   
2020 Agarwal S, Smith M, De La Rosa I, Verba KA, Swartz P, Segura-Totten M, Mattos C. Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor. Acta Crystallographica. Section D, Structural Biology. 76: 1001-1014. PMID 33021502 DOI: 10.1107/S2059798320011341   
2020 Hossain MJ, Rashid MA, Sultan MZ. Transition Metal Chelation Augments the Half-life of Secnidazole: Molecular Docking and Fluorescence Spectroscopic Approaches. Drug Research. PMID 33098081 DOI: 10.1055/a-1252-2322   
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 Szabó G, Pénzes K, Torner B, Fagyas M, Tarr T, Soltész P, Kis G, Antal M, Kappelmayer J. Distinct and overlapping effects of β-glycoprotein I conformational variants in ligand interactions and functional assays. Journal of Immunological Methods. 112877. PMID 33031793 DOI: 10.1016/j.jim.2020.112877   
2020 Kohlberger M, Wildner S, Regl C, Huber CG, Gadermaier G. Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. Plos One. 15: e0241560. PMID 33151990 DOI: 10.1371/journal.pone.0241560   
2020 Gray MD, Deore PS, Chung AJ, Van Riesen AJ, Manderville RA, Prabhakar PS, Wetmore SD. Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching. Bioconjugate Chemistry. PMID 33156614 DOI: 10.1021/acs.bioconjchem.0c00530   
2020 Bolcato G, Bissaro M, Sturlese M, Moro S. Comparing Fragment Binding PosesPrediction Using HSP90 as a Key Study: When Bound Water Makes the Difference. Molecules (Basel, Switzerland). 25. PMID 33053878 DOI: 10.3390/molecules25204651   
2020 Ghode A, Gross LZF, Tee WV, Guarnera E, Berezovsky IN, Biondi RM, Anand GS. Synergistic Allostery in Multiligand-Protein Interactions. Biophysical Journal. 119: 1833-1848. PMID 33086047 DOI: 10.1016/j.bpj.2020.09.019   
2020 Shityakov S, Fischer A, Su KP, Hussein AA, Dandekar T, Broscheit J. Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species. Acs Omega. 5: 25543-25551. PMID 33073080 DOI: 10.1021/acsomega.0c01295   
2020 Fujino Y, Miyagawa T, Torii M, Inoue M, Fujii Y, Okanishi H, Kanai Y, Masui R. Structural changes induced by ligand-binding drastically increase the thermostability of the Ser/Thr protein kinase TpkD from Thermus thermophilus HB8. Febs Letters. PMID 33159808 DOI: 10.1002/1873-3468.13996   
2020 Yan Z, Wang J. Funneled energy landscape unifies principles of protein binding and evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 33067388 DOI: 10.1073/pnas.2013822117   
2020 Gudhka RB, Bilodeau CL, McCallum SA, McCoy MA, Roush DJ, Snyder MA, Cramer SM. Identification of Preferred Multimodal Ligand Binding Regions on IgG1 F using Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Biotechnology and Bioengineering. PMID 33107976 DOI: 10.1002/bit.27611   
2020 Krah A, van der Hoeven B, Mestrom L, Tonin F, Knobel KCC, Bond PJ, McMillan DGG. A second shell residue modulates a conserved ATP-binding site with radically different affinities for ATP. Biochimica Et Biophysica Acta. General Subjects. 1865: 129766. PMID 33069831 DOI: 10.1016/j.bbagen.2020.129766   
2020 Sonar P, Bellucci L, Mossa A, Heidarsson PO, Kragelund BB, Cecconi C. Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein. Biophysical Journal. PMID 33080224 DOI: 10.1016/j.bpj.2020.09.016   
2020 Karlsson E, Paissoni C, Erkelens AM, Tehranizadeh ZA, Sorgenfrei FA, Andersson E, Ye W, Camilloni C, Jemth P. Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. The Journal of Biological Chemistry. PMID 33067355 DOI: 10.1074/jbc.RA120.015645   
2020 Jaiswal G, Kumar V. In-silico design of a potential inhibitor of SARS-CoV-2 S protein. Plos One. 15: e0240004. PMID 33002032 DOI: 10.1371/journal.pone.0240004   
2020 Olotu FA, Omolabi KF, Soliman MES. Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. Informatics in Medicine Unlocked. 21: 100451. PMID 33083517 DOI: 10.1016/j.imu.2020.100451   
2020 Neira JL, Rizzuti B, Jiménez-Alesanco A, Palomino-Schätzlein M, Abián O, Velázquez-Campoy A, Iovanna JL. A Phosphorylation-Induced Switch in the Nuclear Localization Sequence of the Intrinsically Disordered NUPR1 Hampers Binding to Importin. Biomolecules. 10. PMID 32933064 DOI: 10.3390/biom10091313   
2020 Verma K, Mahalapbutr P, Auepattanapong A, Khaikate O, Kuhakarn C, Takahashi K, Rungrotmongkol T. Molecular dynamics simulations of sulfone derivatives in complex with DNA topoisomerase IIα ATPase domain. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 33089727 DOI: 10.1080/07391102.2020.1831961   
2020 Rattila S, Kleefeldt F, Ballesteros A, Beltrame JS, L Ribeiro M, Ergün S, Dveksler G. Pro-angiogenic effects of pregnancy-specific glycoproteins in endothelial and extravillous trophoblast cells. Reproduction (Cambridge, England). 160: 737-750. PMID 33065549 DOI: 10.1530/REP-20-0169   
2020 Wen J, Liao H, Stachowski K, Hempfling JP, Qian Z, Yuan C, Foster MP, Pei D. Rational design of cell-permeable cyclic peptides containing a d-Pro-l-Pro motif. Bioorganic & Medicinal Chemistry. 28: 115711. PMID 33069067 DOI: 10.1016/j.bmc.2020.115711   
2020 Silva SRB, de Lima Neto JX, Fuzo CA, Fulco UL, Vieira DS. A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera. Physical Chemistry Chemical Physics : Pccp. PMID 33164009 DOI: 10.1039/d0cp04415f   
2020 Sharma V, Shing B, Hernandez-Alvarez L, Debnath A, Podust LM. . Molecular Pharmacology. PMID 33008918 DOI: 10.1124/molpharm.120.000092   
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 Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X: Role of Non-Hot Spot Residues. Biochemistry. PMID 33146015 DOI: 10.1021/acs.biochem.0c00661   
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 Oliva F, Flores-Canales JC, Pieraccini S, Morelli CF, Sironi M, Schiøtt B. Simulating Multiple Substrate-Binding Events by γ-Glutamyltransferase Using Accelerated Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 33112625 DOI: 10.1021/acs.jpcb.0c06907   
2020 Strauss MA, Wegner HA. London dispersion in alkane solvents. Angewandte Chemie (International Ed. in English). PMID 33002307 DOI: 10.1002/anie.202012094   
2020 Qiao L, Wang H, He J, Yang S, Chen A. Truncated affinity-improved aptamers for 17β-estradiol determination by AuNPs-based colorimetric aptasensor. Food Chemistry. 340: 128181. PMID 33032145 DOI: 10.1016/j.foodchem.2020.128181   
2020 Guichard G, Cussol L, Mauran L, Buratto J, Belorusova AY, Neuville M, Osz J, Fribourg S, Fremaux J, Dolain C, Goudreau S, Rochel N. Structural basis for α-helix mimicry and inhibition of protein-protein interactions with oligourea foldamers. Angewandte Chemie (International Ed. in English). PMID 32935897 DOI: 10.1002/anie.202008992   
2020 Mukhopadhyay S. The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation. The Journal of Physical Chemistry. B. PMID 33108190 DOI: 10.1021/acs.jpcb.0c07598   
2020 Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. The Journal of Biological Chemistry. 295: 1454-1463. PMID 31848226 DOI: 10.1074/jbc.RA119.011420   
2020 Bessas NC, da Silva LA, Comar Júnior M, de Lima RG. Interaction of nitrosyl ruthenium complexes, [Ru (NH.NHq-R)(tpy)NO] with human serum albumin: a spectroscopic and computational investigation. Luminescence : the Journal of Biological and Chemical Luminescence. PMID 32986923 DOI: 10.1002/bio.3955   
2020 Sampson CDD, Stewart MJ, Mindell JA, Mulligan C. Solvent accessibility changes in a Na-dependent C-dicarboxylate transporter suggest differential substrate effects in a multistep mechanism. The Journal of Biological Chemistry. PMID 33087444 DOI: 10.1074/jbc.RA120.013894   
2020 Meyer EJ, Torpy DJ, Chernykh A, Thaysen-Andersen M, Nenke MA, Lewis J, Rajapaksha H, Rankin W, Polyak SW. Pyrexia and acidosis act independently of neutrophil elastase reactive center loop cleavage to effect cortisol release from corticosteroid-binding globulin. Protein Science : a Publication of the Protein Society. PMID 33085168 DOI: 10.1002/pro.3982   
2020 Sandall CF, Ziehr BK, MacDonald JA. ATP-Binding and Hydrolysis in Inflammasome Activation. Molecules (Basel, Switzerland). 25. PMID 33036374 DOI: 10.3390/molecules25194572   
2020 Mohammad T, Mathur Y, Hassan MI. InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Briefings in Bioinformatics. PMID 33105480 DOI: 10.1093/bib/bbaa279   
2020 Darby JF, Vidler LR, Simpson PJ, Al-Lazikani B, Matthews SJ, Sharp SY, Pearl LH, Hoelder S, Workman P. Solution structure of the Hop TPR2A domain and investigation of target druggability by NMR, biochemical and in silico approaches. Scientific Reports. 10: 16000. PMID 32994435 DOI: 10.1038/s41598-020-71969-w   
2020 Nakamura A, Ishiwata D, Visootsat A, Uchiyama T, Mizutani K, Kaneko S, Murata T, Igarashi K, Iino R. Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases. The Journal of Biological Chemistry. 295: 14606-14617. PMID 32816991 DOI: 10.1074/jbc.RA120.014792   
2020 Teng FY, Jiang ZZ, Huang LY, Guo M, Chen F, Hou XM, Xi XG, Xu Y. A Toolbox for Site-Specific Labeling of RecQ Helicase With a Single Fluorophore Used in the Single-Molecule Assay. Frontiers in Molecular Biosciences. 7: 586450. PMID 33102530 DOI: 10.3389/fmolb.2020.586450