| Year |
Citation |
Score |
| 2023 |
Heid LF, Agerschou ED, Orr AA, Kupreichyk T, Schneider W, Wördehoff MM, Schwarten M, Willbold D, Tamamis P, Stoldt M, Hoyer W. Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation. Computational and Structural Biotechnology Journal. 23: 417-430. PMID 38223341 DOI: 10.1016/j.csbj.2023.12.023 |
0.7 |
|
| 2022 |
Orr AA, Kuhlmann SK, Tamamis P. Computational design of a β-wrapin's N-terminal domain with canonical and non-canonical amino acid modifications mimicking curcumin's proposed inhibitory function. Biophysical Chemistry. 286: 106805. PMID 35417810 DOI: 10.1016/j.bpc.2022.106805 |
0.714 |
|
| 2022 |
Orr AA, Chen Y, Gazit E, Tamamis P. Computational and Experimental Protocols to Study Cyclo-dihistidine Self- and Co-assembly: Minimalistic Bio-assemblies with Enhanced Fluorescence and Drug Encapsulation Properties. Methods in Molecular Biology (Clifton, N.J.). 2405: 179-203. PMID 35298815 DOI: 10.1007/978-1-0716-1855-4_10 |
0.701 |
|
| 2021 |
Hearon SE, Orr AA, Moyer H, Wang M, Tamamis P, Phillips TD. Montmorillonite clay-based sorbents decrease the bioavailability of per- and polyfluoroalkyl substances (PFAS) from soil and their translocation to plants. Environmental Research. 205: 112433. PMID 34875259 DOI: 10.1016/j.envres.2021.112433 |
0.658 |
|
| 2021 |
Aviv M, Cohen-Gerassi D, Orr AA, Misra R, Arnon ZA, Shimon LJW, Shacham-Diamand Y, Tamamis P, Adler-Abramovich L. Modification of a Single Atom Affects the Physical Properties of Double Fluorinated Fmoc-Phe Derivatives. International Journal of Molecular Sciences. 22. PMID 34502542 DOI: 10.3390/ijms22179634 |
0.689 |
|
| 2021 |
Orr AA, Wang M, Beykal B, Ganesh HS, Hearon SE, Pistikopoulos EN, Phillips TD, Tamamis P. Combining Experimental Isotherms, Minimalistic Simulations, and a Model to Understand and Predict Chemical Adsorption onto Montmorillonite Clays. Acs Omega. 6: 14090-14103. PMID 34124432 DOI: 10.1021/acsomega.1c00481 |
0.68 |
|
| 2021 |
Gazit E, Chen Y, Yang Y, Orr AA, Makam P, Redko B, Haimov E, Wang Y, Shimon LJW, Rencus-Lazar S, Ju M, Tamamis P, Dong H. Self-assembled peptide nano-superstructure towards enzyme mimicking hydrolysis. Angewandte Chemie (International Ed. in English). PMID 34014019 DOI: 10.1002/anie.202105830 |
0.72 |
|
| 2021 |
Ben-Zvi O, Grinberg I, Orr AA, Noy D, Tamamis P, Yacoby I, Adler-Abramovich L. Protection of Oxygen-Sensitive Enzymes by Peptide Hydrogel. Acs Nano. PMID 33844499 DOI: 10.1021/acsnano.0c09512 |
0.669 |
|
| 2020 |
Park H, Jin UH, Karki K, Allred C, Davidson LA, Chapkin RS, Orr AA, Nowshad F, Jayaraman A, Tamamis P, Safe S. Hydroxylated Chalcones as Aryl Hydrocarbon Receptor Agonists: Structure-Activity Effects. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 33263770 DOI: 10.1093/toxsci/kfaa179 |
0.683 |
|
| 2020 |
Wang M, Orr AA, Jakubowski JM, Bird KE, Casey CM, Hearon SE, Tamamis P, Phillips TD. Enhanced adsorption of per- and polyfluoroalkyl substances (PFAS) by edible, nutrient-amended montmorillonite clays. Water Research. 188: 116534. PMID 33125992 DOI: 10.1016/j.watres.2020.116534 |
0.679 |
|
| 2020 |
Orr AA, He S, Wang M, Goodall A, Hearon SE, Phillips TD, Tamamis P. Insights into the interactions of bisphenol and phthalate compounds with unamended and carnitine-amended montmorillonite clays. Computers & Chemical Engineering. 143. PMID 33122868 DOI: 10.1016/J.Compchemeng.2020.107063 |
0.703 |
|
| 2020 |
Jakubowski JM, Orr AA, Le DA, Tamamis P. Correction to "Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations". Journal of Chemical Information and Modeling. 60: 4108. PMID 32702234 DOI: 10.1021/Acs.Jcim.0C00784 |
0.713 |
|
| 2020 |
Tao K, Chen Y, Orr AA, Tian Z, Makam P, Gilead S, Si M, Rencus-Lazar S, Qu S, Zhang M, Tamamis P, Gazit E. Enhanced Fluorescence for Bioassembly by Environment-Switching Doping of Metal Ions. Advanced Functional Materials. 30. PMID 32256278 DOI: 10.1002/Adfm.201909614 |
0.699 |
|
| 2020 |
Chen Y, Orr AA, Tao K, Wang Z, Ruggiero A, Shimon LJW, Schnaider L, Goodall A, Rencus-Lazar S, Gilead S, Slutsky I, Tamamis P, Tan Z, Gazit E. High-Efficiency Fluorescence through Bioinspired Supramolecular Self-Assembly. Acs Nano. PMID 32013408 DOI: 10.1021/Acsnano.9B10024 |
0.718 |
|
| 2020 |
Gonzalez-Rivera JC, Orr AA, Engels SM, Jakubowski JM, Sherman MW, O'Connor KN, Matteson T, Woodcock BC, Contreras LM, Tamamis P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Computational and Structural Biotechnology Journal. 18: 137-152. PMID 31988703 DOI: 10.1016/J.Csbj.2019.12.003 |
0.689 |
|
| 2020 |
Jakubowski JM, Orr AA, Le DA, Tamamis P. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. 60: 289-305. PMID 31809572 DOI: 10.1021/Acs.Jcim.9B00561 |
0.761 |
|
| 2019 |
Jonnalagadda SVR, Gerace AJ, Thai K, Johnson J, Tsimenidis K, Jakubowski JM, Shen C, Henderson KJ, Tamamis P, Gkikas M. Amyloid Peptide Scaffolds Coordinate with Alzheimer's Disease Drugs. The Journal of Physical Chemistry. B. PMID 31881810 DOI: 10.1021/Acs.Jpcb.9B10368 |
0.797 |
|
| 2019 |
Kokotidou C, Jonnalagadda SVR, Orr AA, Vrentzos G, Kretsovali A, Tamamis P, Mitraki AA. Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles. Biomolecules. 10. PMID 31861408 DOI: 10.3390/biom10010007 |
0.801 |
|
| 2019 |
Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophysical Journal. PMID 31839263 DOI: 10.1016/J.Bpj.2019.11.3382 |
0.699 |
|
| 2019 |
Wang M, Orr AA, He S, Dalaijamts C, Chiu WA, Tamamis P, Phillips TD. Montmorillonites Can Tightly Bind Glyphosate and Paraquat Reducing Toxin Exposures and Toxicity. Acs Omega. 4: 17702-17713. PMID 31681876 DOI: 10.1021/acsomega.9b02051 |
0.656 |
|
| 2019 |
Park H, Jin UH, Orr AA, Echegaray SP, Davidson LA, Allred CD, Chapkin R, Jayaraman A, Lee K, Tamamis P, Safe SH. Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships. Chemical Research in Toxicology. PMID 31621310 DOI: 10.1021/Acs.Chemrestox.9B00352 |
0.693 |
|
| 2019 |
Yoon K, Chen CC, Orr AA, Barreto PN, Tamamis P, Safe S. Activation of COUP-TFI by a Novel Diindolylmethane Derivative. Cells. 8. PMID 30866413 DOI: 10.3390/Cells8030220 |
0.692 |
|
| 2019 |
Kokotidou C, Tamamis P, Mitraki A. Self‐Assembling Amyloid Sequences as Scaffolds for Material Design: A Case Study of Building Blocks Inspired From the Adenovirus Fiber Protein Macromolecular Symposia. 386: 1900005. DOI: 10.1002/Masy.201900005 |
0.316 |
|
| 2018 |
Orr AA, Shaykhalishahi H, Mirecka EA, Jonnalagadda SVR, Hoyer W, Tamamis P. Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of -wrapins. Computers & Chemical Engineering. 116: 322-332. PMID 30405276 DOI: 10.1016/J.Compchemeng.2018.02.013 |
0.796 |
|
| 2018 |
Mohan RR, Wilson M, Gorham RD, Harrison RES, Morikis VA, Kieslich CA, Orr AA, Coley AV, Tamamis P, Morikis D. Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands. Acs Omega. 3: 6427-6438. PMID 30221234 DOI: 10.1021/acsomega.8b00606 |
0.795 |
|
| 2018 |
Jonnalagadda SVR, Kokotidou C, Orr AA, Fotopoulou E, Henderson KJ, Choi CH, Lim WT, Choi SJ, Jeong HK, Mitraki A, Tamamis P. Computational Design of Functional Amyloid Materials with Cesium Binding, Deposition and Capture Properties. The Journal of Physical Chemistry. B. PMID 29975835 DOI: 10.1021/Acs.Jpcb.8B04103 |
0.792 |
|
| 2018 |
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Tamamis P, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8 |
0.765 |
|
| 2018 |
Kokotidou C, Jonnalagadda SVR, Orr AA, Seoane-Blanco M, Apostolidou CP, van Raaij MJ, Kotzabasaki M, Chatzoudis A, Jakubowski JM, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Llamas-Saiz AL, Tamamis P, et al. A Novel Amyloid Designable Scaffold and Potential Inhibitor Inspired by GAIIG of Amyloid Beta and the HIV-1 V3 loop. Febs Letters. PMID 29772603 DOI: 10.1002/1873-3468.13096 |
0.792 |
|
| 2018 |
Jin UH, Park H, Li X, Davidson LA, Allred C, Patil B, Jayaprakasha G, Orr AA, Mao L, Chapkin RS, Jayaraman A, Tamamis P, Safe S. Structure-Dependent Modulation of Aryl Hydrocarbon Receptor-Mediated Activities by Flavones. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 29584932 DOI: 10.1093/Toxsci/Kfy075 |
0.7 |
|
| 2018 |
Orr AA, Jayaraman A, Tamamis P. Molecular Modeling of Chemoreceptor:Ligand Interactions. Methods in Molecular Biology (Clifton, N.J.). 1729: 353-372. PMID 29429104 DOI: 10.1007/978-1-4939-7577-8_28 |
0.713 |
|
| 2018 |
Orr AA, Gonzalez-Rivera JC, Wilson M, Reena Bhikha P, Wang D, Contreras LM, Tamamis P. "A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins". Methods (San Diego, Calif.). PMID 29408626 DOI: 10.1016/J.Ymeth.2018.01.015 |
0.677 |
|
| 2018 |
Orr AA, Wolfgang H, Tamamis P. O2-02-04: Beta-Wrapin Proteins Sequestering Amyloid Proteins Involved In Alzheimer'S Disease: Understanding Their Function And Designing Novel, Improved Beta-Wrapins As Potential Therapeutics Alzheimers & Dementia. 14. DOI: 10.1016/J.Jalz.2018.06.2648 |
0.691 |
|
| 2017 |
Deidda G, Jonnalagadda SVR, Spies JW, Ranella A, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Tamamis P, Mitraki A. Self-Assembled Amyloid Peptides with Arg-Gly-Asp (RGD) Motifs As Scaffolds for Tissue Engineering. Acs Biomaterials Science & Engineering. 3: 1404-1416. PMID 33429698 DOI: 10.1021/Acsbiomaterials.6B00570 |
0.807 |
|
| 2017 |
Khoury GA, Smadbeck J, Kieslich CA, Koskosidis AJ, Guzman YA, Tamamis P, Floudas CA. Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment. Proteins. PMID 28241391 DOI: 10.1002/Prot.25274 |
0.781 |
|
| 2017 |
Jonnalagadda SVR, Ornithopoulou E, Orr AA, Mossou E, Trevor Forsyth V, Mitchell EP, Bowler MW, Mitraki A, Tamamis P. Computational design of amyloid self-assembling peptides bearing aromatic residues and the cell adhesive motif Arg-Gly-Asp Molecular Systems Design & Engineering. 2: 321-335. DOI: 10.1039/C7ME00016B |
0.798 |
|
| 2016 |
Orr AA, Wördehoff MM, Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. The Journal of Physical Chemistry. B. 120: 12781-12794. PMID 27934063 DOI: 10.1021/Acs.Jpcb.6B08485 |
0.716 |
|
| 2016 |
Cheng Y, Jin UH, Davidson LA, Chapkin RS, Jayaraman A, Tamamis P, Orr A, Allred C, Denison MS, Soshilov A, Weaver E, Safe S. Microbial-Derived 1,4-Dihydroxy-2-naphthoic Acid and Related Compounds as Aryl Hydrocarbon Receptor Agonists/Antagonists: Structure-Activity Relationships and Receptor Modeling. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 27837168 DOI: 10.1093/Toxsci/Kfw230 |
0.691 |
|
| 2016 |
Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism. Plos One. 11: e0148974. PMID 26859389 DOI: 10.1371/Journal.Pone.0148974 |
0.718 |
|
| 2015 |
Gorham RD, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive CK, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. Journal of Medicinal Chemistry. 58: 814-26. PMID 25494040 DOI: 10.1021/Jm501345Y |
0.813 |
|
| 2014 |
Tamamis P, Kasotakis E, Archontis G, Mitraki A. Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides. Methods in Molecular Biology (Clifton, N.J.). 1216: 53-70. PMID 25213410 DOI: 10.1007/978-1-4939-1486-9_3 |
0.742 |
|
| 2014 |
Tamamis P, Kieslich CA, Nikiforovich GV, Woodruff TM, Morikis D, Archontis G. Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking. Bmc Biophysics. 7: 5. PMID 25170421 DOI: 10.1186/2046-1682-7-5 |
0.797 |
|
| 2014 |
Tamamis P, Floudas CA. Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Scientific Reports. 4: 5447. PMID 24965094 DOI: 10.1038/Srep05447 |
0.513 |
|
| 2014 |
Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family. Acs Synthetic Biology. 3: 855-69. PMID 24932669 DOI: 10.1021/Sb400168U |
0.794 |
|
| 2014 |
Tamamis P, Floudas CA. Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop. Plos One. 9: e95767. PMID 24763408 DOI: 10.1371/Journal.Pone.0095767 |
0.487 |
|
| 2014 |
Tamamis P, Floudas CA. Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. Journal of Chemical Information and Modeling. 54: 1174-88. PMID 24660779 DOI: 10.1021/Ci500069Y |
0.497 |
|
| 2014 |
Tamamis P, Terzaki K, Kassinopoulos M, Mastrogiannis L, Mossou E, Forsyth VT, Mitchell EP, Mitraki A, Archontis G. Self-assembly of an aspartate-rich sequence from the adenovirus fiber shaft: insights from molecular dynamics simulations and experiments. The Journal of Physical Chemistry. B. 118: 1765-74. PMID 24437637 DOI: 10.1021/Jp409988N |
0.731 |
|
| 2014 |
Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines. Proteins. 82: 794-814. PMID 24174311 DOI: 10.1002/Prot.24459 |
0.772 |
|
| 2013 |
Tamamis P, Floudas CA. Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop. Biophysical Journal. 105: 1502-14. PMID 24048002 DOI: 10.1016/J.Bpj.2013.07.049 |
0.479 |
|
| 2013 |
Gorham RD, Forest DL, Tamamis P, López de Victoria A, Kraszni M, Kieslich CA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Experimental Eye Research. 116: 96-108. PMID 23954241 DOI: 10.1016/J.Exer.2013.07.023 |
0.811 |
|
| 2012 |
López de Victoria A, Tamamis P, Kieslich CA, Morikis D. Insights into the structure, correlated motions, and electrostatic properties of two HIV-1 gp120 V3 loops. Plos One. 7: e49925. PMID 23185486 DOI: 10.1371/Journal.Pone.0049925 |
0.691 |
|
| 2012 |
Tamamis P, López de Victoria A, Gorham RD, Bellows-Peterson ML, Pierou P, Floudas CA, Morikis D, Archontis G. Molecular dynamics in drug design: new generations of compstatin analogs. Chemical Biology & Drug Design. 79: 703-18. PMID 22233517 DOI: 10.1111/J.1747-0285.2012.01324.X |
0.763 |
|
| 2012 |
A. Kieslich C, Tamamis P, D. Gorham Jr. R, Lopez de Victoria A, U. Sausman N, Archontis G, Morikis D. Exploring Protein-Protein and Protein-Ligand Interactions in the Immune System using Molecular Dynamics and Continuum Electrostatics Current Physical Chemistry. 2: 324-343. DOI: 10.2174/1877946811202040324 |
0.663 |
|
| 2012 |
de Victoria AL, Tamamis P, Gorham RD, Kieslich CA, Bellows-Peterson ML, Floudas CA, Archontis G, Morikis D. Computational and Experimental Analysis of the Interactions Between C3 and Compstatin Family Peptides Biophysical Journal. 102: 62a. DOI: 10.1016/J.Bpj.2011.11.371 |
0.815 |
|
| 2011 |
Tamamis P, Pierou P, Mytidou C, Floudas CA, Morikis D, Archontis G. Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: the case of C3 inhibition by compstatin. Proteins. 79: 3166-79. PMID 21989937 DOI: 10.1002/Prot.23149 |
0.744 |
|
| 2011 |
Pieridou G, Avgousti-Menelaou C, Tamamis P, Archontis G, Hayes SC. UV resonance Raman study of TTR(105-115) structural evolution as a function of temperature. The Journal of Physical Chemistry. B. 115: 4088-98. PMID 21428385 DOI: 10.1021/Jp107519B |
0.696 |
|
| 2011 |
Pieridou G, Avgousti-Menelaou C, Tamamis P, Archontis G, Hayes SC. Correction to “UV Resonance Raman Study of TTR(105–115) Structural Evolution as a Function of Temperature” The Journal of Physical Chemistry B. 115: 9337-9337. DOI: 10.1021/Jp205360X |
0.629 |
|
| 2011 |
Tamamis P, Archontis G. Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations Journal of Non-Crystalline Solids. 357: 717-722. DOI: 10.1016/J.Jnoncrysol.2010.05.083 |
0.725 |
|
| 2010 |
Tamamis P, Morikis D, Floudas CA, Archontis G. Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins. 78: 2655-67. PMID 20589629 DOI: 10.1002/Prot.22780 |
0.737 |
|
| 2009 |
Tamamis P, Kasotakis E, Mitraki A, Archontis G. Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: insights from molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 15639-47. PMID 19863125 DOI: 10.1021/Jp9066718 |
0.748 |
|
| 2009 |
Tamamis P, Adler-Abramovich L, Reches M, Marshall K, Sikorski P, Serpell L, Gazit E, Archontis G. Self-assembly of phenylalanine oligopeptides: insights from experiments and simulations. Biophysical Journal. 96: 5020-9. PMID 19527662 DOI: 10.1016/J.Bpj.2009.03.026 |
0.73 |
|
| 2007 |
Tamamis P, Skourtis SS, Morikis D, Lambris JD, Archontis G. Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water. Journal of Molecular Graphics & Modelling. 26: 571-80. PMID 17498990 DOI: 10.1016/J.Jmgm.2007.03.014 |
0.705 |
|
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