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Morikis Publication List

 

·        Books

·        Book Chapters

·        Review Articles

·        Articles

·        Ph.D. Dissertation

·        Undergraduate Research Publications

·        Electronic Publications

·        Articles in Conference Proceedings

·        Conference Abstracts

·        Published Reports

·        Deposited Structures

Books

1.                Morikis, D., and Lambris, J. D. (Eds.) (2005) Structural Biology of the Complement System, CRC Press/Taylor & Francis Group, Boca Raton, FL (ISBN 0-8247-2540-9). 370 pages. Link. For Book Reviews see: Gordon, D. (2006) Immunology and Cell Biology 84:486, Link; Martinez, O. P. (2006) World Allergy Organization, Link; Tsokos, G. (2005) Clinical Immunology 116:306, Link.

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Book Chapters

2.                Floudas, C. A., Fung, H. K., Morikis, D., Taylor, M. S., and Zhang, L. (2008) Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility, in Mathematical Modeling of Biosystems, Applied Optimization Series, p.p. 133-184, R. P. Mondaini and P. M. Pardalos (Eds.), Springer, New York. Link.

3.                Morikis, D., Floudas, C. A., and Lambris, J. D. (2005) Structure-based integrative computational and experimental approach for the optimization of drug design, in ICCS 2005, Lecture Notes in Computer Science: Computational Science, p.p. 680-688, V. S. Sunderam, G. D. van Albada, P. M. A. Sloot, and J. J. Dongarra (Eds.), Springer-Verlag, Berlin-Heidelberg. Link.

4.                Morikis D., and Lambris, J. D. (2005), The building blocks of the complement system, in Structural Biology of the Complement System, p.p. 1-18, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL. Link.

5.                Morikis D., Holland, M. C. H., and Lambris, J. D. (2005) Structure of the anaphylatoxins C3a and C5a, in Structural Biology of the Complement System, p.p. 161-177, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL. Link.

6.                Morikis D., and Lambris, J. D. (2005) Structure, dynamics, activity, and function of compstatin and design of more potent analogs, in Structural Biology of the Complement System, p.p. 317-340, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL.  Link.

7.                Sahu, A., Morikis, D., and Lambris, J. D. (2000) Complement inhibitors targeting C3, C4, and C5, in Contemporary Immunology: Therapeutic Interventions in the Complement System, p.p. 75-112, J. D. Lambris and V. M. Holers (Eds.), Humana Press Inc., Totowa, New Jersey. Link.

8.                Morikis, D., Newlon, M. G., and Jennings, P. A. (2000) Structure calculations of symmetric dimers using molecular dynamics/simulated annealing and NMR restraints: The case of the RIIa subunit of protein kinase A, in Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, p.p. 141-156, C. A. Floudas and P. M. Pardalos (Eds.), Nonconvex Optimization and its Applications v. 40, Kluwer Academic Publishers, Dordrecht, the Netherlands. Link.

9.                Morikis, D., Sahu, A., Moore, W. T., and Lambris, J. D. (1999) Design, structure, function and application of compstatin, in Bioactive Peptides in Drug Discovery and Design: Medical Aspects, p.p. 235-246, J. Matsoukas and T. Mavromoustakos (Eds.), Biomedical and Health Series, Ios Press, Amsterdam, the Netherlands. Link.

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Review Articles

10.           Mallik, B. and Morikis, D. (2006) Applications of molecular dynamics simulations in immunology: a useful computational method in aiding vaccine design, Current Proteomics 3, 259-270. Link.

11.           Morikis, D., Mallik, B., and Zhang, L. (2006) Biophysical and bioengineering methods for the study of the complement system at atomic resolution, WSEAS Transactions on Biology and Biomedicine 6, 408-413. Link.

12.           Wu, J. and Morikis, D. (2006) Molecular thermodynamics for charged biomacromolecules, Fluid Phase Equilibria 241:317-333. Link. Special Festschrift issue in honor of Professor John M. Prausnitz.

13.           Morikis, D. and Lambris J. D. (2004) Physical methods for structure, dynamics, and binding in immunological research, Trends in Immunology 25:700-707. Link. Special anniversary issue for the 25th year birthday of Immunology Today/Trends in Immunology.

14.           Holland, M. C. H., Morikis, D., and Lambris, J. D. (2004) Synthetic small molecule complement inhibitors, Current Opinion in Investigational Drugs 5, 1164-1173. Link.

15.           Mastellos, D., Morikis, D., Strey, C., Holland, M. C., and Lambris, J. D. (2004) From atoms to systems: a cross-disciplinary approach to complement mediated functions, Molecular Immunology 41:153-164.Link.

16.           Morikis, D., Soulika, A. M., Mallik, B., Klepeis, J. L., Floudas, C. A., and Lambris, J. D. (2004) Improvement of the anti-C3 activity of compstatin using rational and combinatorial approaches, Biochemical Society Transactions 32:28-32. Link.

17.           Mastellos, D., Morikis, D., Isaacs, S. N., Holland, M. C., Strey, C. W., and Lambris, J. D. (2003) Complement: structure, functions, evolution, and viral molecular mimicry, Immunologic Research 27, 367-386. Link.

18.           Morikis, D., and Lambris, J. D. (2002) Structural aspects and design of low-molecular-mass complement inhibitors, Biochemical Society Transactions 30:1026-1036. Link.

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Articles

19.           Galanakis, P. A., Kandias, N., Rizos, A. K., Morikis, D., Krambovitis E., Spyroulias, G. A. (2009) NMR evidence of charge-dependent interaction between various PND V3 and CCR5 N-terminal peptides, Biopolymers: Peptide Science 92:94-109. Link, Suppl.

20.           Zhang, L., Mallik, B., and Morikis, D. (2008) The NMR structure of a cyclic C5aR antagonist, Biopolymers: Peptide Science 90: 803-815. Link, Suppl.

21.           Mallik, B., Zhang, L., Koide, S., and Morikis, D. (2008) pH Dependence of Stability of the 10th Human Fibronectin Type III Domain: A Computational Study, Biotechnology Progress 24:48-55. Link, Suppl. In Special Section: First International Conference on Biomolecular Engineering (ICBE).

22.           Fung, H. K., Floudas, C. A., Taylor, M. S., Zhang, L., and Morikis, D. (2008) Towards full-sequence de novo protein design with flexible templates for human beta-defensin-2, Biophysical Journal 94:584-599. Link, Suppl.

23.           Huynh, N., Mallik, B., Zhang, L., Martins-Green, M., and Morikis, D. (2008) Computational studies of CXCR1, the receptor of IL-8/CXCL8, using molecular dynamics and electrostatics, Biopolymers 89:52-61. Link, Suppl.

24.           Chae, K., Zhang, K., Zhang, L., Morikis, D., Kim, S., Mollet, J.-C., de la Rosa, N., Tan, K., and Lord E. M. (2007) Two SCA (stigma/style cysteine-rich adhesin) isoforms show structural differences that correlate with their levels of in vitro pollen tube adhesion activity, Journal of Biological Chemistry 282:33845-33858. Link, Suppl.

25.           Zhang, L., and Morikis, D. (2007) Solution structure of a bent a-helix, Biochemistry 46:12959-12967. TOC, Link, Suppl.

26.           Tamamis, P., Skourtis, S. S., Morikis, D., Lambris, J. D., and Archontis, G. (2007) Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water, Journal of Molecular Graphics and Modelling 26:571-580. Link, Suppl.

27.           Zhang, L., Mallik, B., and Morikis D. (2007) Immunophysical exploration of C3d-CR2(CCP1-2) association using molecular dynamics and electrostatics, Journal of Molecular Biology 369:567-583. Link, Suppl.

28.           Morikis, D., Rizos, A. K., Spandidos, D., and Krambovitis, E. (2007) Electrostatic modeling of peptides derived from the V3-loop of HIV-1 gp120: implications in the interaction with chemokine receptor CCR5, International Journal of Molecular Medicine 19, 343-352. Link.

29.           Rizos, A. K., Tsikalas, I., Morikis, D., Galanakis, P., Spyroulias, G. A., and Krambovitis, E. (2006) Characterization of the interaction between peptides derived from the gp120/V3 domain of HIV-1 and the amino terminal of the chemokine receptor CCR5 by NMR spectroscopy and light scattering, Journal of Non-Crystalline Solids 352:4451-4458. Link.

30.           Morikis, D., and Zhang, L. (2006) An immunophysical study of the complement system: examples for the pH dependence of protein binding and stability, Journal of Non-Crystalline Solids 352:4445-4450. Link.

31.           Zhang, L., and Morikis D. (2006) Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics, Biophysical Journal 90:3106-3119. Link, Suppl.

32.           Mallik, B. and Morikis D. (2005) Development of a quasi-dynamic pharmacophore model for anti-complement peptide analogs, Journal of the American Chemical Society 127:10967-10976. TOC, Link, Suppl.

33.           Sfyroera, G., Katragadda, M., Morikis, D., Isaacs, S. N., and Lambris, J. D. (2005) Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins, Journal of Immunology 174:2143-2151. Link.

34.           Mallik, B., Katragadda, M., Spruce, L. A., Carafides, C., Tsokos, C. G., Morikis, D., and Lambris J. D. (2005) Design and NMR characterization of active analogs of compstatin containing non-natural amino acids, Journal of Medicinal Chemistry 48:274-286. TOC, Link.

35.           Katragadda, M., Morikis, D., and Lambris, J. D. (2004) Thermodynamic studies on the interaction of the third complement component and its inhibitor compstatin, Journal of Biological Chemistry 279:54987-54995. Link.

36.           Kim, J. H., Morikis, D., and Ozkan, M. (2004) Adaptation of inorganic quantum dots for stable molecular beacons, Sensors and Actuators B-Chemical 102:315-319. Link.

37.           Kim, J. H., Stephens, J. P., Morikis, D., and Ozkan, M. (2004) Hybrid inorganic-organic molecular beacons, Sensor Letters 2, 85-90. Link.

38.           Morikis, D., and Lambris, J. D. (2004) The electrostatic nature of C3d-CR2 association, Journal of Immunology 172:7537-7547. Link, Suppl.

39.           Klepeis, J. L., Floudas, C. A., Morikis, D., Tsokos, C. G., and Lambris, J. D. (2004) Design of peptide analogs with improved activity using a novel de novo protein design approach, Industrial & Engineering Chemistry Research 43:3817-3826. Link. Special issue for Professor Arthur W. Westerberger Festschrift.

40.           Mallik, B., Lambris, J. D., and Morikis, D. (2003) Conformational inter-conversion of compstatin probed with molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics 53:130-141. Link.

41.           Morikis, D., Elcock, A. H., Jennings, P. A., and McCammon, A. J. (2003) The pH dependence of stability of the activation helix and the catalytic site of GART, Biophysical Chemistry 105:279-291. Link, Color Fig. Special issue in honor of Professor Walter J. Kauzmann.

42.           Banky, P., Roy, M., Newlon, M. G. Morikis, D., Haste, N. M., Taylor, S. S., and Jennings, P. A. (2003) Related protein-protein interaction modules present drastically different surface topographies despite a conserved helical platform, Journal of Molecular Biology 330:1117-1129. Link.

43.           Soulika, A. M., Morikis, D., Sarrias, M.-R., Roy, M., Spruce, L. A., Sahu, A., and Lambris, J. D. (2003) Studies of Structure-Activity Relations of Complement Inhibitor Compstatin, Journal of Immunology 170:1881-1890. Link. Erratum: (2004) 172:5128. Link.

44.           Klepeis, J. L., Floudas, C. A., Morikis, D., Tsokos, C. G., Argyropoulos, E., Spruce, L., and Lambris, J. D. (2003) Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity, Journal of the American Chemical Society 125:8422-8423. TOC, Link, Suppl.

45.           Sahu, A., Morikis, D., and Lambris, J. D. (2003) Compstatin, a peptide inhibitor of complement, exhibits species-specific binding to complement component C3. Molecular Immunology 39:557-566. Link.

46.           Morikis, D., Roy, M., Newlon, M. G., Scott, J. D., and Jennings, P. A. (2002) Electrostatic properties of the structure of the docking and dimerization domain of protein kinase A IIa, European Journal of Biochemistry 269, 2040-2051. Link.

47.           Morikis, D., Roy, M., Sahu, A., Troganis, A., Jennings, P. A., Tsokos, G. C., and Lambris J. D. (2002) The structural basis of compstatin activity examined by structure-function-based design of peptide analogs and NMR, Journal of Biological Chemistry 277:14942-14953. Link, Suppl.

48.           Morikis, D., Elcock, A. H., Jennings, P. A., and McCammon, J. A. (2001) Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations, Protein Science 10:2379-2392. Link, Suppl.

49.           Morikis, D., Elcock, A. H., Jennings, P. A., and McCammon, J. A. (2001) Native state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations, Protein Science 10:2363-2378. Link, Suppl.

50.           Newlon, M. G., Roy, M., Morikis, D., Carr, D. W., Westphal, R., Scott, J. D., and Jennings, P. A. (2001) A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes, EMBO Journal 20 , 1651-1662. Link.

51.           Sahu, A., Soulika, A., Morikis, D., Spruce, L., Moore, W. T., and Lambris, J. D. (2000) Binding kinetics, structure-activity relationship, and biotransformation of the complement inhibitor Compstatin, Journal of Immunology 165:2491-2499. Link.

52.           Klepeis, J. L., Floudas, C. A., Morikis, D., and Lambris, J. D. (1999) Predicting peptide structures using NMR data and deterministic global optimization, Journal of Computational Chemistry 20:1354-1370. Link.

53.           Newlon, M. G., Roy, M., Morikis, D., Hausken, Z. E., Coghlan, V., Scott J. D. and Jennings, P. A. (1999) The molecular basis for protein kinase A anchoring revealed by solution NMR, Nature, Structural Biology 6:222-227. Link.

54.           Morikis, D., Assa-Munt, N., Sahu, A., and Lambris, J. D. (1998) Solution structure of compstatin, a potent complement inhibitor, Protein Science 7:619-627. Link, Suppl.

55.           Morikis, D., and Wright, P. E. (1996) Hydrogen exchange in the carbon monoxide complex of soybean leghemoglobin, European Journal of Biochemistry 237 , 212-220. Link.

56.           Brüschweiler, R., Morikis, D., and Wright, P.E. (1995) Hydration of the partially folded peptide RN‑24 studied by multidimensional NMR, Journal of Biomolecular NMR 5:353‑356. Link.

57.           Morikis, D., Lepre, C. A., and Wright, P. E. (1994) 1H resonance assignments and secondary Structure of the carbon monoxide complex of soybean leghemoglobin determined by homonuclear two‑dimensional and three‑dimensional NMR spectroscopy, European Journal of Biochemistry 219 , 611-626. Link.

58.           Merutka, G., Morikis, D., Brüschweiler, R., and Wright, P. E. (1993) NMR evidence for multiple conformations in a highly helical model peptide, Biochemistry 32:13089‑13097. Link.

59.           Morikis, D., Brüschweiler, R., and Wright, P. E. (1993) Determination of local ligand conformations in slowly tumbling proteins by homonuclear 2D and 3D NMR: Application to heme propionates in leghemoglobin, Journal of the American Chemical Society 115:6238‑6246. Link.

60.           Sage, J. T., Morikis, D., Li, P., and Champion, P. M. (1992) Low pH myoglobin photoproducts, Biophysical Journal 61:1041‑1044.  Link.

61.           Zhu, L., Sage, J. T., Rigos, A. A., Morikis, D. and Champion, P. M. (1992) Conformational interconversion in protein crystals, Journal of Molecular Biology 224:207‑215. Link.

62.           Wells, A. V., Sage, J. T., Morikis, D., Champion, P. M., Chiu, M. L., and Sligar, S. G. (1991) The iron‑histidine mode of myoglobin revisited: Resonance Raman studies of isotopically labeled Escherichia coli expressed myoglobin, Journal of the American Chemical Society 113:9655‑9660. Link.

63.           Morikis, D., Li, P., Bangcharoenpaurpong, O., Sage, J. T., and Champion, P.  M. (1991) Resonance Raman scattering as a probe of electron‑nuclear coupling: Applications to heme proteins, Journal of Physical Chemistry 95:3391‑3398. Link.

64.           Sage, J. T., Morikis, D., and Champion, P. M. (1991) Spectroscopic studies of myoglobin at low pH: Heme structure and ligation, Biochemistry 30:1227‑1237. Link.

65.           Egeberg, K. D., Springer, B. A., Martinis, S. A., Sligar, S. G., Morikis, D., and Champion, P. M. (1990) Alteration of sperm whale myoglobin heme axial ligation by site directed mutagenesis, Biochemistry 29:9783‑9791. Link.

66.           Morikis, D., Champion, P. M., Springer, B. A., Egeberg, K. D., and Sligar, S. G. (1990) Resonance Raman studies of iron spin and axial coordination in distal pocket mutants of ferric myoglobin, Journal of Biological Chemistry 265:12143‑12145. Link.

67.           Morikis, D., Champion, P. M., Springer, B. A., and Sligar, S. G. (1989) Resonance Raman investigations of site‑directed mutants of myoglobin: Effects of distal histidine replacement, Biochemistry 28:4791‑4800. Link.

68.           Sage, J. T., Morikis, D., and Champion, P. M. (1989) Resonance Raman studies of oriented chromophores: Metmyoglobin single crystals, Journal of Chemical Physics 90:3015‑3032. Link.

69.           Morikis, D., Sage, J. T., Rizos, A. K., and Champion P. M. (1988) Resonance Raman studies of myoglobin single crystals, Journal of the American Chemical Society 110:6341‑6342. Link.

70.           Sligar, S. G., Egeberg, K. D., Sage, J. T., Morikis, D., and Champion P. M. (1987) Alteration of heme axial ligands by site‑directed mutagenesis: A cytochrome becomes a catalytic demethylase, Journal of the American Chemical Society 109:7896‑7897. Link.

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Ph.D. Dissertation

71.           Morikis, D. (1990) Resonance Raman Investigations of Heme Proteins in the Liquid, Frozen and Crystalline Phase: a Study of the Heme Pocket of Myoglobin, Northeastern University, Boston, MA. 456 pages.

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Undergraduate Research Publications

72.           Cheung, A. S., Yang, J., Kieslich, C. A., Morikis, D. (2008) Computational Prediction of Association Free Energies for the C3d-CR2 Complex and Comparison to Experimental Data, UCR Undergraduate Research Journal 2:13-22. Link.

73.           Morikis, D., Papadopoulou, B., Dimitriadis, S. (1982) Theory of colors and introduction to color photography, Optics Laboratory, Physics Department, Aristotle University of Thessaloniki, Thessaloniki, Greece (in Greek). Undergraduate senior project, 122 pages.

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Electronic Publications

74.           Morikis, D. (2005) CD accompanying the book Structural Biology of the Complement System, CRC Press/Taylor & Francis Group, Boca Raton, FL. Link.

75.           Morikis, D. (2002) UCR biomolecular modeling workshop: hands-on tutorial on structural modeling. Link.

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Articles in Conference Proceedings

76.           Morikis, D., Mallik, B., and Zhang, L. (2006) Biophysical and bioengineering methods for the study of the complement system at atomic resolution. Proceedings of the 2006 WSEAS International Conference on Cellular and Molecular Biology - Biophysics and Bioengineering (BIO’06), p.p. 80-85. Proceedings of the conference held in Vouliagmeni, Athens, Greece, 7/14-16/2006.

77.           Floudas, C. A., Klepeis, J. L., Lambris, J. D., and Morikis, D. (2004) De novo protein design: an interplay of global optimization, mixed-integer optimization and experiments, in FOCAPD 2004, Sixth International Conference on Foundations of Computer-Aided Process Design, Discovery through Product and Process Design, pp. 133-146, C. A. Floudas and R. Agrawal (Eds.), CACHE Corporation, Austin TX. Proceedings of the Conference held at Princeton University, Princeton, NJ, 7/11-16/2004.

78.           Champion, P. M., Morikis, D., Li, P. and Sage, J. T. (1990) Resonance Raman investigations of native and mutant myoglobins, in Proceedings of the XII International Conference on Raman Spectroscopy (ICORS), pp. 664‑665, J. R. Durig and J. F. Sullivan (Eds.), John Wiley and Sons Inc. Proceedings of the Conference held at Columbia, SC, 9/13-17/1990.

79.           Champion, P. M., Morikis, D., Springer, B. and Sligar, S. G. (1988) Resonance Raman studies of site directed mutants and single crystals of myoglobin, in Proceedings of the XI International Conference on Raman Spectroscopy (ICORS), pp. 687‑688, R. J. H. Clark and D. A. Long (Eds.), John Wiley and Sons Inc. Proceedings of the Conference held at London, UK, 9/5‑9/1988.

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Conference Abstracts

80+ Conference abstracts, available upon request.

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Published Reports

80.           Morikis, D. and Champion, P. M. (1986) Resonance Raman Studies of Biological Molecules, in 1985‑1986 Annual Report, Francis Bitter National Magnet Laboratory, p. 81, Massachusetts Institute of Technology.

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Unpublished Work

81.           Morikis, D. (1985-) Various software packages for data analysis and simulations.

82.           Morikis, D. (1982) Introduction to color photography, Thessaloniki, Greece (text for general audience, in Greek). 34 pages.

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Deposited Structures at the Protein Data Bank (PDB) or Biological Magnetic Resonance Bank (BMRB)

83.           BMRB Accession Number 15443 (2007) Structural Study of Ac-Phe-[Orn-Pro-dCha-Trp-Arg], a Potent C5a Receptor Antagonist, by NMR; Zhang, L., Mallik, B., and Morikis, D. Link.

84.           BMRB Accession Number 11005 (2007) Solution structure of a bent alpha-helix; Zhang, L., and Morikis, D. Link.

85.           PDB Code 2H9R (2006) Docking and dimerization domain (D/D) of the regulatory subunit of the Type IIa cAMP-dependent protein kinase A associated with the peptide AKAP75 derived from an A-kinase anchoring protein (AKAP); Newlon, M. G., Roy, M., Morikis, D., Carr, D. W., Westphal, R., Scott, J. D., and Jennings, P. A. Link.

86.           PDB Code 2DRN (2006) Docking and dimerization domain (D/D) of the regulatory subunit of the Type IIa cAMP-dependent protein kinase A associated with the peptide Ht31 derived from an A-kinase anchoring protein (AKAP); Newlon, M. G., Roy, M., Morikis, D., Carr, D. W., Westphal, R., Scott, J. D., and Jennings, P. A. Link.

87.           PDB Code 2EZW (2006) Docking and dimerization domain of the Type Ia regulatory subunit of protein kinase A (RIa D/D); Banky, P., Roy, M., Newlon, M. G., Morikis, D., Haste, N. M., Taylor, S. S., and Jennings, P. A. Link.

88.           PDB Code 1L6E (2002) Docking and dimerization domain of protein kinase A IIa (RIIa D/D); Morikis, D., Newlon, M. G., Scott, J. D., and Jennings, P. A. Link.

89.           PDB Code 1R2A (1998) cAMP-dependent protein kinase Type IIa regulatory subunit (dimerization-anchoring domain); Newlon, M. G., Roy, M., Morikis, D., Hausken, Z. E., Coghlan, V., Scott, J. D., and Jennings, P. A. Link.

90.           PDB Code 1A1P (1998) Compstatin; Morikis, D., Assa-Munt, N., Sahu, A., and Lambris, J. D. Link.

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