Roger Armen

TitleAsst Prof CHP
InstitutionThomas Jefferson University
DepartmentJSP - Pharmaceutical Science
Address901 Walnut Street
Philadelphia PA 19107
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    F32GM076836     (ARMEN, ROGER S)Jan 16, 2006 - Jul 15, 2008
    NIH/NIGMS
    Assessment of protein flexibility in molecular docking
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Chan TO, Armen RS, Yadav S, Shah S, Zhang J, Tiegs BC, Keny N, Blumhof B, Deshpande DA, Rodeck U, Penn RB. A tripartite cooperative mechanism confers resistance of the protein kinase A catalytic subunit to dephosphorylation. J Biol Chem. 2020 Jan 21. PMID: 31964716.
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    2. Cingolani G, Panella A, Perrone MG, Vitale P, Di Mauro G, Fortuna CG, Armen RS, Ferorelli S, Smith WL, Scilimati A. Structural basis for selective inhibition of Cyclooxygenase-1 (COX-1) by diarylisoxazoles mofezolac and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole (P6). Eur J Med Chem. 2017 Jun 24; 138:661-668. PMID: 28710965.
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    3. Sakkal LA, Rajkowski KZ, Armen RS. Prediction of consensus binding mode geometries for related chemical series of positive allosteric modulators of adenosine and muscarinic acetylcholine receptors. J Comput Chem. 2017 Jun 05; 38(15):1209-1228. PMID: 28130813.
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    4. Chan TO, Zhang J, Tiegs BC, Blumhof B, Yan L, Keny N, Penny M, Li X, Pascal JM, Armen RS, Rodeck U, Penn RB. Akt kinase C-terminal modifications control activation loop dephosphorylation and enhance insulin response. Biochem J. 2015 Oct 1; 471(1):37-51. PMID: 26201515.
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    5. Schumann M, Armen RS. Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PLoS One. 2013; 8(12):e83533. PMID: 24391782.
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    6. Steffen JD, Brody JR, Armen RS, Pascal JM. Structural Implications for Selective Targeting of PARPs. Front Oncol. 2013; 3:301. PMID: 24392349.
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    7. Schumann M, Armen RS. Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure. J Comput Chem. 2013 May 30; 34(14):1258-69. PMID: 23420703.
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    8. Estrada T, Zhang B, Cicotti P, Armen RS, Taufer M. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach. Comput Biol Med. 2012 Jul; 42(7):758-71. PMID: 22658682.
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    9. Chan TO, Pascal JM, Armen RS, Rodeck U. Autoregulation of kinase dephosphorylation by ATP binding in AGC protein kinases. Cell Cycle. 2012 Feb 1; 11(3):475-8. PMID: 22262182.
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    10. Zhang M, Pascal JM, Schumann M, Armen RS, Zhang JF. Identification of the functional binding pocket for compounds targeting small-conductance Ca²?-activated potassium channels. Nat Commun. 2012; 3:1021. PMID: 22929778.
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    11. Chan TO, Zhang J, Rodeck U, Pascal JM, Armen RS, Spring M, Dumitru CD, Myers V, Li X, Cheung JY, Feldman AM. Resistance of Akt kinases to dephosphorylation through ATP-dependent conformational plasticity. Proc Natl Acad Sci U S A. 2011 Nov 15; 108(46):E1120-7. PMID: 22031698.
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    12. Rahaman O, Estrada TP, Doren DJ, Taufer M, Brooks CL, Armen RS. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy. J Chem Inf Model. 2011 Sep 26; 51(9):2047-65. PMID: 21644546.
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    13. May ER, Armen RS, Mannan AM, Brooks CL. The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners. Proteins. 2010 Aug 1; 78(10):2251-64. PMID: 20544962.
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    14. Armen RS, Schiller SM, Brooks CL. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes. Proteins. 2010 Jun; 78(8):1926-38. PMID: 20310065.
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    15. Armen RS, Chen J, Brooks CL. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theory Comput. 2009 Oct 13; 5(10):2909-2923. PMID: 20160879.
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    16. Taufer M, Armen R, Chen J, Teller P, Brooks C. Computational multiscale modeling in protein--ligand docking. IEEE Eng Med Biol Mag. 2009 Mar-Apr; 28(2):58-69. PMID: 19349252.
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    17. Steward RE, Armen RS, Daggett V. Different disease-causing mutations in transthyretin trigger the same conformational conversion. Protein Eng Des Sel. 2008 Mar; 21(3):187-95. PMID: 18276611.
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    18. Armen RS, Daggett V. Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology. Biochemistry. 2005 Dec 13; 44(49):16098-107. PMID: 16331970.
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    19. Armen RS, Bernard BM, Day R, Alonso DO, Daggett V. Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13433-8. PMID: 16157882.
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    20. Beck DA, Armen RS, Daggett V. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry. 2005 Jan 18; 44(2):609-16. PMID: 15641786.
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    21. Armen RS, Alonso DO, Daggett V. Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH. Structure. 2004 Oct; 12(10):1847-63. PMID: 15458633.
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    22. Armen RS, DeMarco ML, Alonso DO, Daggett V. Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease. Proc Natl Acad Sci U S A. 2004 Aug 10; 101(32):11622-7. PMID: 15280548.
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    23. Day R, Beck DA, Armen RS, Daggett V. A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. Protein Sci. 2003 Oct; 12(10):2150-60. PMID: 14500873.
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    24. Armen R, Alonso DO, Daggett V. The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions. Protein Sci. 2003 Jun; 12(6):1145-57. PMID: 12761385.
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    25. Goetz DH, Willie ST, Armen RS, Bratt T, Borregaard N, Strong RK. Ligand preference inferred from the structure of neutrophil gelatinase associated lipocalin. Biochemistry. 2000 Feb 29; 39(8):1935-41. PMID: 10684642.
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