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    Fred Cohen, PhD, MD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentCellular Molecular Pharmacology
    Address600 16th Street
    San Francisco CA 94158
    Phone415-476-8519
    vCardDownload vCard

      Collapse Biography 
      Collapse Education and Training
      University of California, San FranciscoPostdoctoral StudiesGraduate Division
      University of California, San Francisco Residency School of Medicine - Internal Medicine

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      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Smith EW, Zhang X, Behzadi C, Andrews LD, Cohen F, Chen Y. Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity. Biochemistry. 2015 Sep 29; 54(38):5937-48. PMID: 26352800.
        View in: PubMed
      2. Patel S, Cohen F, Dean BJ, De La Torre K, Deshmukh G, Estrada AA, Ghosh AS, Gibbons P, Gustafson A, Huestis MP, Le Pichon CE, Lin H, Liu W, Liu X, Liu Y, Ly CQ, Lyssikatos JP, Ma C, Scearce-Levie K, Shin YG, Solanoy H, Stark KL, Wang J, Wang B, Zhao X, Lewcock JW, Siu M. Discovery of dual leucine zipper kinase (DLK, MAP3K12) inhibitors with activity in neurodegeneration models. J Med Chem. 2015 Jan 8; 58(1):401-18. PMID: 25341110.
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      3. Colby DW, Wain R, Baskakov IV, Legname G, Palmer CG, Nguyen HO, Lemus A, Cohen FE, DeArmond SJ, Prusiner SB. Protease-sensitive synthetic prions. PLoS Pathog. 2010 Jan; 6(1):e1000736. PMID: 20107515; PMCID: PMC2809756.
      4. Choi JH, May BC, Wille H, Cohen FE. Molecular modeling of the misfolded insulin subunit and amyloid fibril. Biophys J. 2009 Dec 16; 97(12):3187-95. PMID: 20006956; PMCID: PMC2793351.
      5. Wille H, Bian W, McDonald M, Kendall A, Colby DW, Bloch L, Ollesch J, Borovinskiy AL, Cohen FE, Prusiner SB, Stubbs G. Natural and synthetic prion structure from X-ray fiber diffraction. Proc Natl Acad Sci U S A. 2009 Oct 6; 106(40):16990-5. PMID: 19805070; PMCID: PMC2761340.
      6. Choi JH, May BC, Govaerts C, Cohen FE. Site-directed mutagenesis demonstrates the plasticity of the beta helix: implications for the structure of the misfolded prion protein. Structure. 2009 Jul 15; 17(7):1014-23. PMID: 19604481.
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      7. Choi JH, Govaerts C, May BC, Cohen FE. Analysis of the sequence and structural features of the left-handed beta-helical fold. Proteins. 2008 Oct; 73(1):150-60. PMID: 18398908.
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      8. Tamgüney G, Giles K, Glidden DV, Lessard P, Wille H, Tremblay P, Groth DF, Yehiely F, Korth C, Moore RC, Tatzelt J, Rubinstein E, Boucheix C, Yang X, Stanley P, Lisanti MP, Dwek RA, Rudd PM, Moskovitz J, Epstein CJ, Cruz TD, Kuziel WA, Maeda N, Sap J, Ashe KH, Carlson GA, Tesseur I, Wyss-Coray T, Mucke L, Weisgraber KH, Mahley RW, Cohen FE, Prusiner SB. Genes contributing to prion pathogenesis. J Gen Virol. 2008 Jul; 89(Pt 7):1777-88. PMID: 18559949; PMCID: PMC2828448.
      9. Ghaemmaghami S, Phuan PW, Perkins B, Ullman J, May BC, Cohen FE, Prusiner SB. Cell division modulates prion accumulation in cultured cells. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):17971-6. PMID: 17989223; PMCID: PMC2084281.
      10. Wille H, Govaerts C, Borovinskiy A, Latawiec D, Downing KH, Cohen FE, Prusiner SB. Electron crystallography of the scrapie prion protein complexed with heavy metals. Arch Biochem Biophys. 2007 Nov 15; 467(2):239-48. PMID: 17935686; PMCID: PMC3557509.
      11. Phuan PW, Zorn JA, Safar J, Giles K, Prusiner SB, Cohen FE, May BC. Discriminating between cellular and misfolded prion protein by using affinity to 9-aminoacridine compounds. J Gen Virol. 2007 Apr; 88(Pt 4):1392-401. PMID: 17374787.
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      12. Caffrey CR, Steverding D, Swenerton RK, Kelly B, Walshe D, Debnath A, Zhou YM, Doyle PS, Fafarman AT, Zorn JA, Land KM, Beauchene J, Schreiber K, Moll H, Ponte-Sucre A, Schirmeister T, Saravanamuthu A, Fairlamb AH, Cohen FE, McKerrow JH, Weisman JL, May BC. Bis-acridines as lead antiparasitic agents: structure-activity analysis of a discrete compound library in vitro. Antimicrob Agents Chemother. 2007 Jun; 51(6):2164-72. PMID: 17371810; PMCID: PMC1891397.
      13. Lee LC, Horn F, Cohen FE. Automatic extraction of protein point mutations using a graph bigram association. PLoS Comput Biol. 2007 Feb 2; 3(2):e16. PMID: 17274683; PMCID: PMC1794323.
      14. May BC, Zorn JA, Witkop J, Sherrill J, Wallace AC, Legname G, Prusiner SB, Cohen FE. Structure-activity relationship study of prion inhibition by 2-aminopyridine-3,5-dicarbonitrile-based compounds: parallel synthesis, bioactivity, and in vitro pharmacokinetics. J Med Chem. 2007 Jan 11; 50(1):65-73. PMID: 17201410.
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      15. Legname G, Nguyen HO, Peretz D, Cohen FE, DeArmond SJ, Prusiner SB. Continuum of prion protein structures enciphers a multitude of prion isolate-specified phenotypes. Proc Natl Acad Sci U S A. 2006 Dec 12; 103(50):19105-10. PMID: 17142317; PMCID: PMC1748184.
      16. May BC, Witkop J, Sherrill J, Anderson MO, Madrid PB, Zorn JA, Prusiner SB, Cohen FE, Guy RK. Structure-activity relationship study of 9-aminoacridine compounds in scrapie-infected neuroblastoma cells. Bioorg Med Chem Lett. 2006 Sep 15; 16(18):4913-6. PMID: 16860557.
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      17. Luginbühl B, Kanyo Z, Jones RM, Fletterick RJ, Prusiner SB, Cohen FE, Williamson RA, Burton DR, Plückthun A. Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. J Mol Biol. 2006 Oct 13; 363(1):75-97. PMID: 16962610.
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      18. Weisman JL, Liou AP, Shelat AA, Cohen FE, Guy RK, DeRisi JL. Searching for new antimalarial therapeutics amongst known drugs. Chem Biol Drug Des. 2006 Jun; 67(6):409-16. PMID: 16882315; PMCID: PMC1592519.
      19. May BC, Govaerts C, Cohen FE. Developing therapeutics for the diseases of protein misfolding. Neurology. 2006 Jan 24; 66(2 Suppl 1):S118-22. PMID: 16432139.
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      20. Ye S, Huang Y, Müllendorff K, Dong L, Giedt G, Meng EC, Cohen FE, Kuntz ID, Weisgraber KH, Mahley RW. Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target. Proc Natl Acad Sci U S A. 2005 Dec 20; 102(51):18700-5. PMID: 16344478; PMCID: PMC1311738.
      21. Legname G, Nguyen HO, Baskakov IV, Cohen FE, Dearmond SJ, Prusiner SB. Strain-specified characteristics of mouse synthetic prions. Proc Natl Acad Sci U S A. 2005 Feb 8; 102(6):2168-73. PMID: 15671162; PMCID: PMC548557.
      22. Legname G, Baskakov IV, Nguyen HO, Riesner D, Cohen FE, DeArmond SJ, Prusiner SB. Synthetic mammalian prions. Science. 2004 Jul 30; 305(5684):673-6. PMID: 15286374.
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      23. Govaerts C, Wille H, Prusiner SB, Cohen FE. Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Natl Acad Sci U S A. 2004 Jun 1; 101(22):8342-7. PMID: 15155909; PMCID: PMC420396.
      24. Schmitt-Ulms G, Hansen K, Liu J, Cowdrey C, Yang J, DeArmond SJ, Cohen FE, Prusiner SB, Baldwin MA. Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues. Nat Biotechnol. 2004 Jun; 22(6):724-31. PMID: 15146195.
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      25. May BC, Govaerts C, Prusiner SB, Cohen FE. Prions: so many fibers, so little infectivity. Trends Biochem Sci. 2004 Apr; 29(4):162-5. PMID: 15124628.
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      26. Tremblay P, Ball HL, Kaneko K, Groth D, Hegde RS, Cohen FE, DeArmond SJ, Prusiner SB, Safar JG. Mutant PrPSc conformers induced by a synthetic peptide and several prion strains. J Virol. 2004 Feb; 78(4):2088-99. PMID: 14747574; PMCID: PMC369494.
      27. Horn F, Lau AL, Cohen FE. Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors. Bioinformatics. 2004 Mar 1; 20(4):557-68. PMID: 14990452.
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      28. Cohen FE, Kelly JW. Therapeutic approaches to protein-misfolding diseases. Nature. 2003 Dec 18; 426(6968):905-9. PMID: 14685252.
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      29. Chandonia JM, Cohen FE. New local potential useful for genome annotation and 3D modeling. J Mol Biol. 2003 Sep 26; 332(4):835-50. PMID: 12972255.
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      30. May BC, Fafarman AT, Hong SB, Rogers M, Deady LW, Prusiner SB, Cohen FE. Potent inhibition of scrapie prion replication in cultured cells by bis-acridines. Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6):3416-21. PMID: 12626750; PMCID: PMC152307.
      31. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 2003; 4(2):R9. PMID: 12620119; PMCID: PMC151308.
      32. Devoto A, Hartmann HA, Piffanelli P, Elliott C, Simmons C, Taramino G, Goh CS, Cohen FE, Emerson BC, Schulze-Lefert P, Panstruga R. Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family. J Mol Evol. 2003 Jan; 56(1):77-88. PMID: 12569425.
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      33. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res. 2003 Jan 1; 31(1):294-7. PMID: 12520006; PMCID: PMC165550.
      34. Joachimiak MP, Cohen FE. JEvTrace: refinement and variations of the evolutionary trace in JAVA. Genome Biol. 2002; 3(12):RESEARCH0077. PMID: 12537566; PMCID: PMC151179.
      35. Goh CS, Cohen FE. Co-evolutionary analysis reveals insights into protein-protein interactions. J Mol Biol. 2002 Nov 15; 324(1):177-92. PMID: 12421567.
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      36. Perrier V, Kaneko K, Safar J, Vergara J, Tremblay P, DeArmond SJ, Cohen FE, Prusiner SB, Wallace AC. Dominant-negative inhibition of prion replication in transgenic mice. Proc Natl Acad Sci U S A. 2002 Oct 1; 99(20):13079-84. PMID: 12271119; PMCID: PMC130589.
      37. Du X, Guo C, Hansell E, Doyle PS, Caffrey CR, Holler TP, McKerrow JH, Cohen FE. Synthesis and structure-activity relationship study of potent trypanocidal thio semicarbazone inhibitors of the trypanosomal cysteine protease cruzain. J Med Chem. 2002 Jun 20; 45(13):2695-707. PMID: 12061873.
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      38. Rodrigues CR, Flaherty TM, Springer C, McKerrow JH, Cohen FE. CoMFA and HQSAR of acylhydrazide cruzain inhibitors. Bioorg Med Chem Lett. 2002 Jun 3; 12(11):1537-41. PMID: 12031337.
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      39. Burkoth TS, Beausoleil E, Kaur S, Tang D, Cohen FE, Zuckermann RN. Toward the synthesis of artificial proteins: the discovery of an amphiphilic helical peptoid assembly. Chem Biol. 2002 May; 9(5):647-54. PMID: 12031671.
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      40. Baskakov IV, Legname G, Baldwin MA, Prusiner SB, Cohen FE. Pathway complexity of prion protein assembly into amyloid. J Biol Chem. 2002 Jun 14; 277(24):21140-8. PMID: 11912192.
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      41. Wille H, Michelitsch MD, Guenebaut V, Supattapone S, Serban A, Cohen FE, Agard DA, Prusiner SB. Structural studies of the scrapie prion protein by electron crystallography. Proc Natl Acad Sci U S A. 2002 Mar 19; 99(6):3563-8. PMID: 11891310; PMCID: PMC122563.
      42. Caffrey CR, Schanz M, Nkemngu NJ, Nkemgu-Njinkeng J, Brush M, Hansell E, Cohen FE, Flaherty TM, McKerrow JH, Steverding D. Screening of acyl hydrazide proteinase inhibitors for antiparasitic activity against Trypanosoma brucei. Int J Antimicrob Agents. 2002 Mar; 19(3):227-31. PMID: 11932146.
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      43. Nicholson EM, Mo H, Prusiner SB, Cohen FE, Marqusee S. Differences between the prion protein and its homolog Doppel: a partially structured state with implications for scrapie formation. J Mol Biol. 2002 Feb 22; 316(3):807-15. PMID: 11866533.
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      44. Avery MA, Alvim-Gaston M, Rodrigues CR, Barreiro EJ, Cohen FE, Sabnis YA, Woolfrey JR. Structure-activity relationships of the antimalarial agent artemisinin. 6. The development of predictive in vitro potency models using CoMFA and HQSAR methodologies. J Med Chem. 2002 Jan 17; 45(2):292-303. PMID: 11784134.
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      45. Beisser PS, Goh CS, Cohen FE, Michelson S. Viral chemokine receptors and chemokines in human cytomegalovirus trafficking and interaction with the immune system. CMV chemokine receptors. Curr Top Microbiol Immunol. 2002; 269:203-34. PMID: 12224510.
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      46. Schmitt-Ulms G, Legname G, Baldwin MA, Ball HL, Bradon N, Bosque PJ, Crossin KL, Edelman GM, DeArmond SJ, Cohen FE, Prusiner SB. Binding of neural cell adhesion molecules (N-CAMs) to the cellular prion protein. J Mol Biol. 2001 Dec 14; 314(5):1209-25. PMID: 11743735.
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      47. Ball HL, King DS, Cohen FE, Prusiner SB, Baldwin MA. Engineering the prion protein using chemical synthesis. J Pept Res. 2001 Nov; 58(5):357-74. PMID: 11892845.
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      48. Joachimiak MP, Chang C, Rosenthal PJ, Cohen FE. The impact of whole genome sequence data on drug discovery--a malaria case study. Mol Med. 2001 Oct; 7(10):698-710. PMID: 11713369; PMCID: PMC1949995.
      49. Laws DD, Bitter HM, Liu K, Ball HL, Kaneko K, Wille H, Cohen FE, Prusiner SB, Pines A, Wemmer DE. Solid-state NMR studies of the secondary structure of a mutant prion protein fragment of 55 residues that induces neurodegeneration. Proc Natl Acad Sci U S A. 2001 Sep 25; 98(20):11686-90. PMID: 11562491; PMCID: PMC58790.
      50. Korth C, May BC, Cohen FE, Prusiner SB. Acridine and phenothiazine derivatives as pharmacotherapeutics for prion disease. Proc Natl Acad Sci U S A. 2001 Aug 14; 98(17):9836-41. PMID: 11504948; PMCID: PMC55539.
      51. Matsunaga Y, Peretz D, Williamson A, Burton D, Mehlhorn I, Groth D, Cohen FE, Prusiner SB, Baldwin MA. Cryptic epitopes in N-terminally truncated prion protein are exposed in the full-length molecule: dependence of conformation on pH. Proteins. 2001 Aug 1; 44(2):110-8. PMID: 11391773.
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      52. Baskakov IV, Legname G, Prusiner SB, Cohen FE. Folding of prion protein to its native alpha-helical conformation is under kinetic control. J Biol Chem. 2001 Jun 8; 276(23):19687-90. PMID: 11306559.
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      53. Peretz D, Scott MR, Groth D, Williamson RA, Burton DR, Cohen FE, Prusiner SB. Strain-specified relative conformational stability of the scrapie prion protein. Protein Sci. 2001 Apr; 10(4):854-63. PMID: 11274476; PMCID: PMC2373967.
      54. Supattapone S, Wille H, Uyechi L, Safar J, Tremblay P, Szoka FC, Cohen FE, Prusiner SB, Scott MR. Branched polyamines cure prion-infected neuroblastoma cells. J Virol. 2001 Apr; 75(7):3453-61. PMID: 11238871; PMCID: PMC114138.
      55. Harrison PM, Chan HS, Prusiner SB, Cohen FE. Conformational propagation with prion-like characteristics in a simple model of protein folding. Protein Sci. 2001 Apr; 10(4):819-35. PMID: 11274473; PMCID: PMC2373973.
      56. Supattapone S, Bouzamondo E, Ball HL, Wille H, Nguyen HO, Cohen FE, DeArmond SJ, Prusiner SB, Scott M. A protease-resistant 61-residue prion peptide causes neurodegeneration in transgenic mice. Mol Cell Biol. 2001 Apr; 21(7):2608-16. PMID: 11259607; PMCID: PMC86891.
      57. Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol. 2001 Mar 23; 307(2):721-35. PMID: 11254392.
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      58. Viles JH, Donne D, Kroon G, Prusiner SB, Cohen FE, Dyson HJ, Wright PE. Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Biochemistry. 2001 Mar 6; 40(9):2743-53. PMID: 11258885.
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      59. Alonso DO, DeArmond SJ, Cohen FE, Daggett V. Mapping the early steps in the pH-induced conformational conversion of the prion protein. Proc Natl Acad Sci U S A. 2001 Mar 13; 98(6):2985-9. PMID: 11248018; PMCID: PMC30593.
      60. Mo H, Moore RC, Cohen FE, Westaway D, Prusiner SB, Wright PE, Dyson HJ. Two different neurodegenerative diseases caused by proteins with similar structures. Proc Natl Acad Sci U S A. 2001 Feb 27; 98(5):2352-7. PMID: 11226243; PMCID: PMC30142.
      61. Supattapone S, Muramoto T, Legname G, Mehlhorn I, Cohen FE, DeArmond SJ, Prusiner SB, Scott MR. Identification of two prion protein regions that modify scrapie incubation time. J Virol. 2001 Feb; 75(3):1408-13. PMID: 11152514; PMCID: PMC114047.
      62. Horn F, Vriend G, Cohen FE. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res. 2001 Jan 1; 29(1):346-9. PMID: 11125133; PMCID: PMC29816.
      63. Supattapone S, Nguyen HO, Muramoto T, Cohen FE, DeArmond SJ, Prusiner SB, Scott M. Affinity-tagged miniprion derivatives spontaneously adopt protease-resistant conformations. J Virol. 2000 Dec; 74(24):11928-34. PMID: 11090193; PMCID: PMC112476.
      64. Aronoff-Spencer E, Burns CS, Avdievich NI, Gerfen GJ, Peisach J, Antholine WE, Ball HL, Cohen FE, Prusiner SB, Millhauser GL. Identification of the Cu2+ binding sites in the N-terminal domain of the prion protein by EPR and CD spectroscopy. Biochemistry. 2000 Nov 14; 39(45):13760-71. PMID: 11076515; PMCID: PMC2903970.
      65. Bogan AA, Dallas-Yang Q, Ruse MD, Maeda Y, Jiang G, Nepomuceno L, Scanlan TS, Cohen FE, Sladek FM. Analysis of protein dimerization and ligand binding of orphan receptor HNF4alpha. J Mol Biol. 2000 Sep 29; 302(4):831-51. PMID: 10993727.
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      66. Silverman GL, Qin K, Moore RC, Yang Y, Mastrangelo P, Tremblay P, Prusiner SB, Cohen FE, Westaway D. Doppel is an N-glycosylated, glycosylphosphatidylinositol-anchored protein. Expression in testis and ectopic production in the brains of Prnp(0/0) mice predisposed to Purkinje cell loss. J Biol Chem. 2000 Sep 1; 275(35):26834-41. PMID: 10842180.
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      67. Du X, Hansell E, Engel JC, Caffrey CR, Cohen FE, McKerrow JH. Aryl ureas represent a new class of anti-trypanosomal agents. Chem Biol. 2000 Sep; 7(9):733-42. PMID: 10980453.
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      68. Troeberg L, Chen X, Flaherty TM, Morty RE, Cheng M, Hua H, Springer C, McKerrow JH, Kenyon GL, Lonsdale-Eccles JD, Coetzer TH, Cohen FE. Chalcone, acyl hydrazide, and related amides kill cultured Trypanosoma brucei brucei. Mol Med. 2000 Aug; 6(8):660-9. PMID: 11055585; PMCID: PMC1949976.
      69. Cohen FE. Prions, peptides and protein misfolding. Mol Med Today. 2000 Jul; 6(7):292-3. PMID: 10859566.
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      70. Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. Co-evolution of proteins with their interaction partners. J Mol Biol. 2000 Jun 2; 299(2):283-93. PMID: 10860738.
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      71. Wille H, Prusiner SB, Cohen FE. Scrapie infectivity is independent of amyloid staining properties of the N-terminally truncated prion protein. J Struct Biol. 2000 Jun; 130(2-3):323-38. PMID: 10940236.
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      72. Perrier V, Wallace AC, Kaneko K, Safar J, Prusiner SB, Cohen FE. Mimicking dominant negative inhibition of prion replication through structure-based drug design. Proc Natl Acad Sci U S A. 2000 May 23; 97(11):6073-8. PMID: 10823951; PMCID: PMC18560.
      73. Zulianello L, Kaneko K, Scott M, Erpel S, Han D, Cohen FE, Prusiner SB. Dominant-negative inhibition of prion formation diminished by deletion mutagenesis of the prion protein. J Virol. 2000 May; 74(9):4351-60. PMID: 10756050; PMCID: PMC111952.
      74. Baskakov IV, Aagaard C, Mehlhorn I, Wille H, Groth D, Baldwin MA, Prusiner SB, Cohen FE. Self-assembly of recombinant prion protein of 106 residues. Biochemistry. 2000 Mar 14; 39(10):2792-804. PMID: 10704232.
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      75. Whittal RM, Ball HL, Cohen FE, Burlingame AL, Prusiner SB, Baldwin MA. Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry. Protein Sci. 2000 Feb; 9(2):332-43. PMID: 10716185; PMCID: PMC2144551.
      76. Kaneko K, Ball HL, Wille H, Zhang H, Groth D, Torchia M, Tremblay P, Safar J, Prusiner SB, DeArmond SJ, Baldwin MA, Cohen FE. A synthetic peptide initiates Gerstmann-Sträussler-Scheinker (GSS) disease in transgenic mice. J Mol Biol. 2000 Jan 28; 295(4):997-1007. PMID: 10656806.
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      77. Safar J, Cohen FE, Prusiner SB. Quantitative traits of prion strains are enciphered in the conformation of the prion protein. Arch Virol Suppl. 2000; (16):227-35. PMID: 11214926.
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      78. Supattapone S, Nguyen HO, Cohen FE, Prusiner SB, Scott MR. Elimination of prions by branched polyamines and implications for therapeutics. Proc Natl Acad Sci U S A. 1999 Dec 7; 96(25):14529-34. PMID: 10588739; PMCID: PMC24470.
      79. Kanyo ZF, Pan KM, Williamson RA, Burton DR, Prusiner SB, Fletterick RJ, Cohen FE. Antibody binding defines a structure for an epitope that participates in the PrPC-->PrPSc conformational change. J Mol Biol. 1999 Nov 5; 293(4):855-63. PMID: 10543972.
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      80. Cohen FE. Protein misfolding and prion diseases. J Mol Biol. 1999 Oct 22; 293(2):313-20. PMID: 10550211.
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      81. Moore RC, Lee IY, Silverman GL, Harrison PM, Strome R, Heinrich C, Karunaratne A, Pasternak SH, Chishti MA, Liang Y, Mastrangelo P, Wang K, Smit AF, Katamine S, Carlson GA, Cohen FE, Prusiner SB, Melton DW, Tremblay P, Hood LE, Westaway D. Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel. J Mol Biol. 1999 Oct 1; 292(4):797-817. PMID: 10525406.
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      82. Liu H, Farr-Jones S, Ulyanov NB, Llinas M, Marqusee S, Groth D, Cohen FE, Prusiner SB, James TL. Solution structure of Syrian hamster prion protein rPrP(90-231). Biochemistry. 1999 Apr 27; 38(17):5362-77. PMID: 10220323.
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      83. Schwartz HL, Chandonia JM, Kash SF, Kanaani J, Tunnell E, Domingo A, Cohen FE, Banga JP, Madec AM, Richter W, Baekkeskov S. High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase. J Mol Biol. 1999 Apr 16; 287(5):983-99. PMID: 10222205.
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      84. Supattapone S, Bosque P, Muramoto T, Wille H, Aagaard C, Peretz D, Nguyen HO, Heinrich C, Torchia M, Safar J, Cohen FE, DeArmond SJ, Prusiner SB, Scott M. Prion protein of 106 residues creates an artifical transmission barrier for prion replication in transgenic mice. Cell. 1999 Mar 19; 96(6):869-78. PMID: 10102274.
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      85. Viles JH, Cohen FE, Prusiner SB, Goodin DB, Wright PE, Dyson HJ. Copper binding to the prion protein: structural implications of four identical cooperative binding sites. Proc Natl Acad Sci U S A. 1999 Mar 2; 96(5):2042-7. PMID: 10051591; PMCID: PMC26733.
      86. Harrison PM, Chan HS, Prusiner SB, Cohen FE. Thermodynamics of model prions and its implications for the problem of prion protein folding. J Mol Biol. 1999 Feb 19; 286(2):593-606. PMID: 9973573.
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      87. Walther D, Cohen FE. Conformational attractors on the Ramachandran map. Acta Crystallogr D Biol Crystallogr. 1999 Feb; 55(Pt 2):506-17. PMID: 10089363.
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      88. Gerloff DL, Cannarozzi GM, Joachimiak M, Cohen FE, Schreiber D, Benner SA. Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins. Biochem Biophys Res Commun. 1999 Jan 8; 254(1):70-6. PMID: 9920734.
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      89. Nguyen JT, Turck CW, Cohen FE, Zuckermann RN, Lim WA. Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science. 1998 Dec 11; 282(5396):2088-92. PMID: 9851931.
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      90. Walther D, Springer C, Cohen FE. Helix-helix packing angle preferences for finite helix axes. Proteins. 1998 Dec 1; 33(4):457-9. PMID: 9849932.
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      91. Gerloff DL, Joachimiak M, Cohen FE, Cannarozzi GM, Chamberlin SG, Benner SA. Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family. Biochem Biophys Res Commun. 1998 Oct 9; 251(1):173-81. PMID: 9790926.
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      95. Huang CY, Uno T, Murphy JE, Lee S, Hamer JD, Escobedo JA, Cohen FE, Radhakrishnan R, Dwarki V, Zuckermann RN. Lipitoids--novel cationic lipids for cellular delivery of plasmid DNA in vitro. Chem Biol. 1998 Jun; 5(6):345-54. PMID: 9653553.
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      105. DeArmond SJ, Sánchez H, Yehiely F, Qiu Y, Ninchak-Casey A, Daggett V, Camerino AP, Cayetano J, Rogers M, Groth D, Torchia M, Tremblay P, Scott MR, Cohen FE, Prusiner SB. Selective neuronal targeting in prion disease. Neuron. 1997 Dec; 19(6):1337-48. PMID: 9427256.
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      106. Selzer PM, Chen X, Chan VJ, Cheng M, Kenyon GL, Kuntz ID, Sakanari JA, Cohen FE, McKerrow JH. Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors. Exp Parasitol. 1997 Nov; 87(3):212-21. PMID: 9371086.
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      107. Byington CL, Dunbrack RL, Whitby FG, Cohen FE, Agabian N. Entamoeba histolytica: computer-assisted modeling of phosphofructokinase for the prediction of broad-spectrum antiparasitic agents. Exp Parasitol. 1997 Nov; 87(3):194-202. PMID: 9371084.
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      108. Peretz D, Williamson RA, Matsunaga Y, Serban H, Pinilla C, Bastidas RB, Rozenshteyn R, James TL, Houghten RA, Cohen FE, Prusiner SB, Burton DR. A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform. J Mol Biol. 1997 Oct 31; 273(3):614-22. PMID: 9356250.
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      113. Muramoto T, DeArmond SJ, Scott M, Telling GC, Cohen FE, Prusiner SB. Heritable disorder resembling neuronal storage disease in mice expressing prion protein with deletion of an alpha-helix. Nat Med. 1997 Jul; 3(7):750-5. PMID: 9212101.
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      114. Lundberg KM, Stenland CJ, Cohen FE, Prusiner SB, Millhauser GL. Kinetics and mechanism of amyloid formation by the prion protein H1 peptide as determined by time-dependent ESR. Chem Biol. 1997 May; 4(5):345-55. PMID: 9195875.
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      116. Telling GC, Tremblay P, Torchia M, Dearmond SJ, Cohen FE, Prusiner SB. N-terminally tagged prion protein supports prion propagation in transgenic mice. Protein Sci. 1997 Apr; 6(4):825-33. PMID: 9098892; PMCID: PMC2144756.
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      118. Kaneko K, Vey M, Scott M, Pilkuhn S, Cohen FE, Prusiner SB. COOH-terminal sequence of the cellular prion protein directs subcellular trafficking and controls conversion into the scrapie isoform. Proc Natl Acad Sci U S A. 1997 Mar 18; 94(6):2333-8. PMID: 9122195; PMCID: PMC20088.
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      120. Gerloff DL, Cohen FE, Benner SA. A predicted consensus structure for the C terminus of the beta and gamma chains of fibrinogen. Proteins. 1997 Feb; 27(2):279-89. PMID: 9061791.
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      122. Schätzl HM, Da Costa M, Taylor L, Cohen FE, Prusiner SB. Prion protein gene variation among primates. J Mol Biol. 1997 Jan 17; 265(2):257. PMID: 9020986.
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      123. Armand P, Kirshenbaum K, Falicov A, Dunbrack RL, Dill KA, Zuckermann RN, Cohen FE. Chiral N-substituted glycines can form stable helical conformations. Fold Des. 1997; 2(6):369-75. PMID: 9427011.
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      124. Byington CL, Dunbrack RL, Cohen FE, Agabian N. Molecular modeling of phosphofructokinase from Entamoeba histolytica for the prediction of new antiparasitic agents. Arch Med Res. 1997; 28 Spec No:86-8. PMID: 9033023.
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      125. Dunbrack RL, Gerloff DL, Bower M, Chen X, Lichtarge O, Cohen FE. Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996. Fold Des. 1997; 2(2):R27-42. PMID: 9135979.
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      126. Yehiely F, Bamborough P, Da Costa M, Perry BJ, Thinakaran G, Cohen FE, Carlson GA, Prusiner SB. Identification of candidate proteins binding to prion protein. Neurobiol Dis. 1997; 3(4):339-55. PMID: 9173930.
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      127. Muramoto T, Scott M, Cohen FE, Prusiner SB. Recombinant scrapie-like prion protein of 106 amino acids is soluble. Proc Natl Acad Sci U S A. 1996 Dec 24; 93(26):15457-62. PMID: 8986833; PMCID: PMC26426.
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      129. Li R, Chen X, Gong B, Selzer PM, Li Z, Davidson E, Kurzban G, Miller RE, Nuzum EO, McKerrow JH, Fletterick RJ, Gillmor SA, Craik CS, Kuntz ID, Cohen FE, Kenyon GL. Structure-based design of parasitic protease inhibitors. Bioorg Med Chem. 1996 Sep; 4(9):1421-7. PMID: 8894100.
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      130. Lichtarge O, Bourne HR, Cohen FE. Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. Proc Natl Acad Sci U S A. 1996 Jul 23; 93(15):7507-11. PMID: 8755504; PMCID: PMC38775.
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      133. Lane NE, Kimmel DB, Nilsson MH, Cohen FE, Newton S, Nissenson RA, Strewler GJ. Bone-selective analogs of human PTH(1-34) increase bone formation in an ovariectomized rat model. J Bone Miner Res. 1996 May; 11(5):614-25. PMID: 9157776.
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      138. Gerloff DL, Cohen FE. Secondary structure prediction and unrefined tertiary structure prediction for cyclin A, B, and D. Proteins. 1996 Jan; 24(1):18-34. PMID: 8628731.
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      149. Nanevicz T, Ishii M, Wang L, Chen M, Chen J, Turck CW, Cohen FE, Coughlin SR. Mechanisms of thrombin receptor agonist specificity. Chimeric receptors and complementary mutations identify an agonist recognition site. J Biol Chem. 1995 Sep 15; 270(37):21619-25. PMID: 7665575.
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      154. Kazmirski SL, Alonso DO, Cohen FE, Prusiner SB, Daggett V. Theoretical studies of sequence effects on the conformational properties of a fragment of the prion protein: implications for scrapie formation. Chem Biol. 1995 May; 2(5):305-15. PMID: 9383432.
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      158. Rosenthal PJ, Ring CS, Chen X, Cohen FE. Characterization of a Plasmodium vivax cysteine proteinase gene identifies uniquely conserved amino acids that may mediate the substrate specificity of malarial hemoglobinases. J Mol Biol. 1994 Aug 12; 241(2):312-6. PMID: 8057374.
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      159. Hunt NG, Gregoret LM, Cohen FE. The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search. J Mol Biol. 1994 Aug 12; 241(2):214-25. PMID: 8057361.
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      160. Ma S, McGregor MJ, Cohen FE, Pallai PV. Conformation of CD4-derived cyclic hexapeptides by NMR and molecular dynamics. Biopolymers. 1994 Aug; 34(8):987-1000. PMID: 8075393.
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      163. Baldwin MA, Pan KM, Nguyen J, Huang Z, Groth D, Serban A, Gasset M, Mehlhorn I, Fletterick RJ, Cohen FE. Spectroscopic characterization of conformational differences between PrPC and PrPSc: an alpha-helix to beta-sheet transition. Philos Trans R Soc Lond B Biol Sci. 1994 Mar 29; 343(1306):435-41. PMID: 7913763.
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      164. Harris NL, Presnell SR, Cohen FE. Four helix bundle diversity in globular proteins. J Mol Biol. 1994 Mar 11; 236(5):1356-68. PMID: 8126725.
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      165. Jin L, Cohen FE, Wells JA. Structure from function: screening structural models with functional data. Proc Natl Acad Sci U S A. 1994 Jan 4; 91(1):113-7. PMID: 7506411; PMCID: PMC42896.
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      173. Ring CS, Cohen FE. Modeling protein structures: construction and their applications. FASEB J. 1993 Jun; 7(9):783-90. PMID: 8330685.
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      185. Curtis BM, Presnell SR, Srinivasan S, Sassenfeld H, Klinke R, Jeffery E, Cosman D, March CJ, Cohen FE. Experimental and theoretical studies of the three-dimensional structure of human interleukin-4. Proteins. 1991; 11(2):111-9. PMID: 1946344.
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      192. Landgraf B, Cohen FE, Smith KA, Gadski R, Ciardelli TL. Structural significance of the C-terminal amphiphilic helix of interleukin-2. J Biol Chem. 1989 Jan 15; 264(2):816-22. PMID: 2783421.
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      196. Cohen FE, Kuntz ID. Prediction of the three-dimensional structure of human growth hormone. Proteins. 1987; 2(2):162-6. PMID: 3447173.
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      197. Hurle MR, Matthews CR, Cohen FE, Kuntz ID, Toumadje A, Johnson WC. Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase. Proteins. 1987; 2(3):210-24. PMID: 3328862.
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      200. Blanar MA, Kneller D, Clark AJ, Karu AE, Cohen FE, Langridge R, Kuntz ID. A model for the core structure of the Escherichia coli RecA protein. Cold Spring Harb Symp Quant Biol. 1984; 49:507-11. PMID: 6397305.
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      202. Sternberg MJ, Cohen FE, Taylor WR. A combinational approach to the prediction of the tertiary fold of globular proteins. Biochem Soc Trans. 1982 Oct; 10(5):299-301. PMID: 6183155.
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      203. Sternberg MJ, Cohen FE. Interferon: a tertiary structure predicted from amino acid sequences. Philos Trans R Soc Lond B Biol Sci. 1982 Sep 24; 299(1094):125-7. PMID: 6183687.
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      204. Cohen FE, Sternberg MJ, Taylor WR. Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins. J Mol Biol. 1982 Apr 25; 156(4):821-62. PMID: 7120396.
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      205. Sternberg MJ, Cohen FE, Taylor WR, Feldmann RJ. Analysis and predication of structural motifs in the glycolytic enzymes. Philos Trans R Soc Lond B Biol Sci. 1981 Jun 26; 293(1063):177-89. PMID: 6115417.
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      206. Cohen FE, Sternberg MJ, Taylor WR. Analysis of the tertiary structure of protein beta-sheet sandwiches. J Mol Biol. 1981 May 25; 148(3):253-72. PMID: 7299817.
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      207. Cohen FE, Novotný J, Sternberg MJ, Campbell DG, Williams AF. Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance. Biochem J. 1981 Apr 1; 195(1):31-40. PMID: 6118138; PMCID: PMC1162852.
      208. Cohen FE, Sternberg MJ, Phillips DC, Kuntz ID, Kollman PA. A diffusion--collision--adhesion model for the kinetics of myoglobin refolding. Nature. 1980 Aug 7; 286(5773):632-4. PMID: 7402344.
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      209. Cohen FE, Sternberg MJ, Taylor WR. Analysis and prediction of protein beta-sheet structures by a combinatorial approach. Nature. 1980 Jun 5; 285(5764):378-82. PMID: 6991952.
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      210. Cohen FE, Sternberg MJ. On the prediction of protein structure: The significance of the root-mean-square deviation. J Mol Biol. 1980 Apr; 138(2):321-33. PMID: 7411610.
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      211. Cohen FE, Sternberg MJ. On the use of chemically derived distance constraints in the prediction of protein structure with myoglobin as an example. J Mol Biol. 1980 Feb 15; 137(1):9-22. PMID: 7365797.
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      212. Cohen FE, Richmond TJ, Richards FM. Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J Mol Biol. 1979 Aug 15; 132(3):275-88. PMID: 533892.
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