SI denotes Supplementary Information online.

1. Harrison RES, Morikis D (2018). Molecular mechanisms of macular degeneration associated with the complement Factor H Y402H mutation, Biophysical Journal, in press.DOI: https://doi.org/10.1016/j.bpj.2018.12.007. SI.
2. Zewde N, Mohan RR, Morikis D (2018) Immunophysical evaluation of the initiating step in the formation of the membrane attack complex, Frontiers in Physics 6:130 (17 pages). DOI: 10.3389/fphy.2018.00130. SI.
3. Malik-Chaudhry HK, Gaieb Z, Saavedra A, Reyes M, Kung R, Le F, Morikis D, Liao J (2018) Dissecting distinct roles of NEDDylation E1 ligase heterodimer APPBP1 and UBA3 reveals potential evolution process for activation of ubiquitin-related pathways, Scientific Reports 8: 10108 (10 pages). DOI: 10.1038/s41598-018-28214-2. SI.
4. Ngo-Duc T-T, Plank JM, Chen G, Harrison RES, Morikis D, Liu H, Haberer ED (2018) M13 bacteriophage spheroids as scaffolds for directed synthesis of spiky gold nanostructures, Nanoscale, View Online. DOI: 10.1039/c8nr03229g. SI.
5. Mohan RR, Wilson M, Gorham RD Jr, Harrison RES, Morikis VA, Kieslich CA, Orr AA, Coley AV, Tamamis P, Morikis D (2018) Virtual screening of chemical compounds for discovery of complement C3 ligands, ACS Omega 3:6427–6438. DOI: 10.1021/acsomega.8b00606. SI.
6. Zewde N, Morikis D (2018) A Computational Model for the Evaluation of Complement System Regulation under Homeostasis, Disease, and Drug Intervention, PLOS ONE 13(6): e0198644 (28 pages, 177 pages supplementary information). https://doi.org/10.1371/journal.pone.0198644. SI.
7. Zewde N, Morikis D (2017) A Computational Model for the Evaluation of Complement System Regulation under Homeostasis, Disease, and Drug Intervention, bioRxiv doi: 10.1101/225029. SI.
8. Harrison RES, Mohan RR, Gorham RD Jr, Kieslich CA, Morikis D (2017) AESOP: A Python Library for Investigating Electrostatics in Protein Interactions, Biophysical Journal 112:1761-1766. DOI: http://dx.doi.org/10.1016/j.bpj.2017.04.005.
9. Gaieb Z, Morikis D (2017) Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding, Journal of Molecular Graphics and Modelling 74:352-358. DOI: http://doi.org/10.1016/j.jmgm.2017.04.012.
10. López-Perrote A, Harrison RES, Subías M, Alcorlo M, Rodríguez de Córdoba S, Morikis D, Llorca O (2017) Ionic tethering contributes to the conformational stability and function of complement C3b, Molecular Immunology 85:137-147. DOI: http://dx.doi.org/10.1016/j.molimm.2016.12.015.
11. Gaieb Z, Morikis D (2017) Detection of side chain rearrangements mediating the motions of transmembrane helices in molecular dynamics simulations of G protein-coupled receptors, Computational and Structural Biotechnology Journal 15:131-137. DOI: http://dx.doi.org/10.1016/j.csbj.2017.01.001.
12. Mohan RR, Cabrera AP, Harrison RES, Gorham RD Jr, Johnson LV, Ghosh K, Morikis D (2016) Peptide Redesign for Inhibition of the complement system: Targeting age-related macular degeneration, Molecular Vision 22:1280-1290. DOI: www.molvis.org/molvis/v22/1280/. SI (2 Appendices).
13. Gaieb Z, Lo DD, Morikis D (2016) Molecular mechanism of biased ligand conformational changes in CC chemokine receptor 7, Journal of Chemical Information and Modeling, 56:1808–1822.  DOI: 10.1021/acs.jcim.6b00367. SI. Paper is featured in journal cover.
14. Croker DE, Monk PN, Halai R, Kaeslin G, Schofield Z, Wu MCL, Clark RJ, Blaskovich MAT, Morikis D, Floudas CA, Cooper MA, Woodruff TM (2016) Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signaling, Immunology & Cell Biology 94:787-795.  DOI: 10.1038/icb.2016.43. Featured Article. News and Commentary: Kember C (2016) Targeting the Dark Horse of complement: the first generation of functionally selective C5aR2 ligands, Immunology & Cell Biology 94:717-718.  DOI: 10.1038/icb.2016.62.
15. Mohan RR, Huber GA, Morikis D (2016) Electrostatic steering accelerates C3d:CR2 association, Journal of Physical Chemistry B 120:8416-8423.  DOI: 10.1021/acs.jpcb.6b02095. Special issue for Professor J. Andrew McCammon Festschrift.
16. Zewde N, Gorham RD Jr, Dorado A, Morikis D (2016) Quantitative modeling of the alternative pathway of the complement system, PLOS ONE 11:e0152337 (26 pages, 43 pages supplementary information).  DOI: 10.1371/journal.pone.0152337. SI.
17. Zhang C, Brown MQ, van de Ven W, Zhang Z-M, Wu B, Young MC, Synek L, Borchardt D, Harrison R, Pan S, Luo N, Huang Y-M, Ghang Y-J, Ung N, Li R, Isley J, Morikis D, Song J, Guo W, Hooley RJ, Chang C, Yang Z, Zarsky V, Muday GK, Hicks GR, Raikhel NV (2016) Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis, Proceedings of the National Academy of Sciences (USA) 113:E41-E50.  DOI: 10.1073/pnas.1521248112. SI.
18. Gorham RD Jr, Nuñez V, Lin J-H, Rooijakkers SHM, Vullev VI, Morikis D (2015) Discovery of small molecules for fluorescent detection of complement system activation product C3d, Journal of Medicinal Chemistry 58:9535-9545.  DOI: 10.1021/acs.jmedchem.5b01062. SI.
19. Chen C, Gorham RD Jr., Gaieb Z, and Morikis D (2015) Electrostatic interactions between complement regulator CD46(SCR1-2) and adenovirus Ad11/Ad21 fiber protein knob, Molecular Biology International, 2015: Article ID 967465. 15 pages. DOI:10.1155/2015/967465. SI.  
20. Bennett KM, Gorham RD, Gusti V, Trinh L, Morikis D, Lo DD (2015) Hybrid flagellin as a T cell independent vaccine scaffold, BMC Biotechnology 15:71.  DOI: 10.1186/s12896-015-0194-0. SI.  
21. Harrison RES, Gorham RD Jr, Morikis D (2015) Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex, Protein Science 24:789-802. DOI:10.1002/pro.2650. SI.  
22. Gorham RD Jr, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive CK, Floudas CA, Radeke MJ, Johnson LV, Morikis D (2015) New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics, Journal of Medicinal Chemistry 58:814-826. DOI: 10.1021/jm501345y. SI.  
23. Mohan R, Gorham RD Jr, Morikis D (2015) A theoretical view of the C3d:CR2 binding controversy, Molecular Immunology 64:112:122. DOI:10.1016/j.molimm.2014.11.006. SI (includes 3 videos).
24. Halai R, Bellows-Peterson ML, Branchett, W, Smadbeck J, Kieslich CA, Croker DE, Cooper MA, Morikis D, Woodruff TM, Floudas CA, Monk PN (2014) Derivation of ligands for the complement C3a receptor from the C-terminus of C5a, European Journal of Pharmacology 745:176-181. DOI: 10.1016/j.ejphar.2014.10.041. SI.
25. Tamamis P, Kieslich CA, Nikiforovich GV, Woodruff TM, Morikis D, Archontis G (2014) Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking, BMC Biophysics 7:5 (16 pages). DOI: 10.1186/2046-1682-7-5. SI, Movie.
26. Liu Y, Kieslich CA, Morikis D, Liao J (2014) Engineering pre-SUMO4 as efficient substrate of SENP2, Protein Engineering Design & Selection 27:117-126. DOI: 10.1093/protein/gzu004.  DOI: 10.1093/protein/gzu004.  
27. Gorham RD Jr, Rodriguez W, Morikis D (2014) Molecular analysis of the interaction between staphylococcal virulence factor Sbi-IV and complement C3d, Biophysical Journal 106:1164-1173. DOI: 10.1016/j.bpj.2014.01.033. SI (includes 3 videos).
28. Kieslich CA, Shin D, López de Victoria A, González-Rivera G, Morikis D (2013) A predictive model for HIV type 1 coreceptor selectivity, AIDS Research & Human Retroviruses 29:1386-1394. DOI: 10.1089/aid.2012.0173. SI.  
29. Gorham Jr RD, Forest DL, Tamamis P, López de Victoria A, Mazák-Kraszni M, Kieslich CA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D (2013) Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures, Experimental Eye Research 116:96-108.  DOI: 10.1016/j.exer.2013.07.023. SI.  
30. Kieslich CA, Morikis D (2012) The two sides of complement C3d: evolution of electrostatics in a  between innate and adaptive immunity, PLoS Computational Biology 8:e1002840 (8 pages). DOI: 10.1371/journal.pcbi.1002840. SI.  
31. López de Victoria A, Tamamis P, Kieslich CA, Morikis D (2012) Insights into the structure, correlated motions, and electrostatic properties of two HIV-1 gp120 V3 loops, PLoS ONE 7:e49925 (15 pages).  DOI: 10.1371/journal.pone.0049925. SI.  
32. Bellows-Peterson ML, Fung H, Floudas CA, Kieslich CA, Zhang L, Morikis D, Wareham KJ, Monk PN, Hawksworth O, Woodruff TM (2012) De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation, Journal of Medicinal Chemistry 55:4159-4168.  DOI: 10.1021/jm201609k. SI.  
33. Tamamis P, López de Victoria A, Gorham Jr RD, Bellows-Peterson ML, Pierrou P, Floudas CA, Morikis D, Archontis G, (2012) Molecular dynamics in drug design: new generations of compstatin analogs, Chemical Biology & Drug Design 79:703-718.  DOI: 10.1021/jm201609k. SI.  
34. López de Victoria A, Kieslich CA, Rizos AK, Krambovitis E, Morikis D (2012) Clustering of HIV-1 subtypes based on gp120 V3 loop electrostatic properties, BMC Biophysics 5:3 (16 pages).  DOI: 10.1186/2046-1682-5-3. SI.  
35. Gorham Jr RD, Kieslich CA, Morikis D (2012) Complement inhibition by Staphylococcus aureus: electrostatics of C3d-EfbC and C3d-Ehp association, Cellular and Molecular Bioengineering 5:32-43. DOI: 10.1007/s12195-011-0195-6. SI. 
36. Gorham Jr RD, Kieslich CA, Nichols A, Sausman NU, Foronda M, Morikis D (2011) An evaluation of Poisson-Boltzmann electrostatic free energy calculations through comparison with experimental mutagenesis data, Biopolymers 95:746-754. DOI: 10.1002/bip.21644. SI.  
37. Tamamis P, Pierou P, Mytidou C, Floudas CA, Morikis D, Archontis G (2011) Design of a modified mouse protein with ligand binding properties of its human analog using molecular dynamics simulations: the case of C3 inhibition by compstatin, Proteins, Structure, Function, Bioinformatics 79:3166-3179.  DOI: 10.1002/prot.23149. SI (includes 2 videos).
38. El-Assaad AM, Kieslich CA, Gorham Jr RD, Morikis D (2011) Electrostatic exploration of the C3d-FH4 interaction using a computational alanine scan, Molecular Immunology 48:1844-1850. DOI: 10.1016/j.molimm.2011.05.007. SI. Erratum (2013) 53:173-174. DOI: 10.1016/j.molimm.2011.05.007.
39. Hakkoymaz H, Kieslich CA, Gorham Jr RD, Gunopulos D, Morikis D (2011) Electrostatic similarity determination using multi-resolution analysis, Molecular Informatics 30:733-746.  DOI: 10.1002/minf.201100002. SI.  
40. Kieslich CA, Vazquez H, Goodman GN, López de Victoria A, Morikis D (2011) The effect of electrostatics on Factor H function and related pathologies, Journal of Molecular Graphics and Modeling 29:1047-1055. DOI: 10.1016/j.jmgm.2011.04.010. SI.  
41. López de Victoria A, Gorham Jr RD, Bellows-Peterson ML, Ling J, Lo D, Floudas CA, Morikis D (2011) A new generation of potent complement inhibitors of the compstatin family, Chemical Biology & Drug Design 77:431-440. DOI: 10.1111/j.1747-0285.2011.01111.x.
42. Kieslich CA, Morikis D, Yang J, Gunopulos D (2011) Automated computational framework for the analysis of electrostatic similarities of proteins, Biotechnology Progress 27:316-325. DOI: 10.1002/btpr.541.
43. Kieslich CA, Gorham Jr RD, Morikis D (2011) Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar, Journal of Non-Crystalline Solids 357:707–716. DOI: 10.1016/j.jnoncrysol.2010.05.087.
44. Qureshi NN, Morikis D, Schiller NL (2011) Contribution of specific amino acid changes in penicillin binding protein 1 to amoxicillin resistance in clinical Helicobacter pylori isolates, Antimicrobial Agents and Chemotherapy 55:101-109.  DOI: 10.1128/AAC.00545-10.
45. Chae K, Gonong BJ, Kim SC, Kieslich CA, Morikis D, Balasubramanian S, Lord EM (2010) A multifaceted study of stigma/style cysteine-rich adhesion (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction, Journal of Experimental Botany 61:4277-4290.  DOI: 10.1093/jxb/erq228. SI.  
46. Tamamis P, Morikis D, Floudas CA, Archontis G (2010) Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations, Proteins, Structure, Function, Bioinformatics 78:2655-2667. DOI: 10.1002/prot.22780. SI (includes 2 videos).
47. Bellows ML, Fung HK, Taylor MS, Floudas CA, López de Victoria A, Morikis D (2010) New compstatin variants through two de novo protein design frameworks, Biophysical Journal 98:2337-2346.  DOI: 10.1016/j.bpj.2010.01.057. SI.  
48. Cheung AS, Kieslich CA, Yang J, Morikis D, (2010) Solvation effects in calculated electrostatic association free energies for the C3d-CR2 complex, and comparison to experimental data, Biopolymers 93:509-519. DOI: 10.1002/bip.21388. Paper is featured in journal cover.
49. Pyaram K, Kieslich CA, Yadav VN, Morikis D, Sahu A (2010) Influence of electrostatics on the complement regulatory functions of kaposica, the complement inhibitor of Kaposi’s sarcoma-associated herpesvirus, Journal of Immunology 184:1956–1967. DOI: 10.4049/​jimmunol.0903261.
50. Chae K, Kieslich CA, Morikis D, Kim SC, Lord EM (2009) A Gain-of-Function Mutation of Arabidopsis Lipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization, Plant Cell 21: 3902–3914.  DOI:10.1105/tpc.109.070854. SI.  
51. Galanakis PA, Kandias N, Rizos AK, Morikis D, Krambovitis E, Spyroulias GA (2009) NMR evidence of charge-dependent interaction between various PND V3 and CCR5 N-terminal peptides, Biopolymers: Peptide Science 92:94-109.  DOI: 10.1002/bip.21127. SI.
52. Zhang L, Mallik B, Morikis D (2008) The NMR structure of a cyclic C5aR antagonist, Biopolymers: Peptide Science 90: 803-815.  DOI: 10.1021/bp0700915. SI.
53. Mallik B, Zhang L, Koide S, Morikis D (2008) pH Dependence of Stability of the 10th Human Fibronectin Type III Domain: A Computational Study, Biotechnology Progress 24:48-55. In Special Section: First International Conference on Biomolecular Engineering (ICBE).  DOI: 10.1021/bp0700915. SI.
54. Fung HK, Floudas CA, Taylor MS, Zhang L, Morikis D (2008) Towards full-sequence de novo protein design with flexible templates for human beta-defensin-2, Biophysical Journal 94:584-599.  DOI: 10.1016/j.bpj.2010.01.057. SI.
55. Huynh N, Mallik B, Zhang L, Martins-Green M, Morikis D (2008) Computational studies of CXCR1, the receptor of IL-8/CXCL8, using molecular dynamics and electrostatics, Biopolymers 89:52-61. DOI: 10.1002/bip.20851. SI.  
56. Chae K, Zhang K, Zhang L, Morikis D, Kim S, Mollet JC, de la Rosa N, Tan K, Lord EM (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. DOI: 10.1074/jbc.M703997200. SI.  
57. Zhang L, Morikis D (2007) Solution structure of a bent α-helix, Biochemistry 46:12959-12967.  DOI: 10.1021/bi701252n. SI.
58. Tamamis P, Skourtis SS, Morikis D, Lambris JD, Archontis G (2007) Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water, Journal of Molecular Graphics and Modelling 26:571-580. DOI: 10.1016/j.jmgm.2007.03.014. SI.  
59. Zhang L, Mallik B, Morikis D (2007) Immunophysical exploration of C3d-CR2(CCP1-2) association using molecular dynamics and electrostatics, Journal of Molecular Biology 369:567-583. DOI: 10.1016/j.jmb.2007.02.101. SI.  
60. Morikis D, Rizos AK, Spandidos D, 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. Paper is featured in journal cover.
61. Rizos AK, Tsikalas I, Morikis D, Galanakis P, Spyroulias, GA, 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. DOI: https://doi.org/10.1016/j.jnoncrysol.2006.01.137.
62. Morikis D, 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. DOI: https://doi.org/10.1016/j.jnoncrysol.2006.01.104.
63. Zhang L, 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. DOI: 10.1529/biophysj.105.068130. SI.  
64. Mallik B, Morikis D (2005) Development of a quasi-dynamic pharmacophore model for anti-complement peptide analogs, Journal of the American Chemical Society 127:10967-10976.  DOI: 10.1021/ja051004c. SI.   
65. Sfyroera G, Katragadda M, Morikis D, Isaacs SN, Lambris JD (2005) Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins, Journal of Immunology 174:2143-2151. DOI: 10.4049/​jimmunol.174.4.2143.
66. Mallik B, Katragadda M, Spruce LA, Carafides C, Tsokos CG, Morikis D, Lambris JD (2005) Design and NMR characterization of active analogs of compstatin containing non-natural amino acids, Journal of Medicinal Chemistry 48:274-286. DOI: 10.1021/jm0495531.
67. Katragadda M, Morikis D, Lambris JD (2004) Thermodynamic studies on the interaction of the third complement component and its inhibitor compstatin, Journal of Biological Chemistry 279:54987-54995. DOI: 10.1074/jbc.M409963200.
68. Kim JH, Morikis D, Ozkan M (2004) Adaptation of inorganic quantum dots for stable molecular beacons, Sensors and Actuators B-Chemical 102:315-319. DOI: 10.1016/j.snb.2004.04.107.
69. Kim JH, Stephens JP, Morikis D, Ozkan M (2004) Hybrid inorganic-organic molecular beacons, Sensor Letters 2:85-90. DOI: 10.1166/sl.2004.042. Paper is featured in journal cover.
70. Morikis D, Lambris JD (2004) The electrostatic nature of C3d-CR2 association, Journal of Immunology 172:7537-7547. DOI: 10.4049/​jimmunol.172.12.7537. SI.
71. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Lambris JD (2004) Design of peptide analogs with improved activity using a novel de novo protein design approach, Industrial & Engineering Chemistry Research 43:3817-3826.  DOI: 10.1021/ie0340995. Special issue for Professor Arthur W. Westerberger Festschrift.
72. Mallik B, Lambris JD, Morikis D (2003) Conformational inter-conversion of compstatin probed with molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics 53:130-141. DOI: 10.1002/prot.10491.
73. Morikis D, Elcock AH, Jennings PA, McCammon AJ (2003) The pH dependence of stability of the activation helix and the catalytic site of GART, Biophysical Chemistry 105:279-291. DOI: 10.1016/S0301-4622(03)00079-6.Color Fig. Special issue in honor of Professor Walter J. Kauzmann.
74. Banky P, Roy M, Newlon MG, Morikis D, Haste NM, Taylor SS, Jennings PA (2003) Related protein-protein interaction modules present drastically different surface topographies despite a conserved helical platform, Journal of Molecular Biology 330:1117-1129.  DOI: 10.1016/S0022-2836(03)00552-7.
75. Soulika AM, Morikis D, Sarrias MR, Roy M, Spruce LA, Sahu A, Lambris JD (2003) Studies of Structure-Activity Relations of Complement Inhibitor Compstatin, Journal of Immunology 170:1881-1890.  DOI: 10.4049/​jimmunol.171.4.1881. Erratum: (2004) 172:5128.  DOI: 10.4049/​jimmunol.172.8.5128.
76. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Argyropoulos E, Spruce L, Lambris JD (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. DOI: 10.1021/ja034846p. SI.  
77. Sahu A, Morikis D, Lambris JD (2003) Compstatin, a peptide inhibitor of complement, exhibits species-specific binding to complement component C3. Molecular Immunology 39:557-566. DOI: 10.1016/S0161-5890(02)00212-2.
78. Morikis D, Roy M, Newlon MG, Scott JD, Jennings PA (2002) Electrostatic properties of the structure of the docking and dimerization domain of protein kinase A IIα, European Journal of Biochemistry 269:2040-1051.  DOI: 10.1046/j.1432-1033.2002.02852.x.
79. Morikis D, Roy M, Sahu A, Troganis A, Jennings PA, Tsokos GC, Lambris JD (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.  DOI: 0.1074/jbc.M200021200. SI.
80. Morikis D, Elcock AH, Jennings PA, McCammon JA (2001) Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations, Protein Science 10:2379-2392.  DOI: 10.1110/ps.17201. SI.
81. Morikis D, Elcock AH, Jennings PA, McCammon JA (2001) Native state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations, Protein Science 10:2363-2378. DOI: 10.1110/ps.17201. SI.
82. Newlon MG, Roy M, Morikis D, Carr DW, Westphal R, Scott JD, Jennings PA (2001) A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes, EMBO Journal 20:1651-1662. DOI: 10.1093/emboj/20.7.1651. Paper is featured in journal cover.
83. Sahu A, Soulika A, Morikis D, Spruce L, Moore WT, Lambris JD (2000) Binding kinetics, structure-activity relationship, and biotransformation of the complement inhibitor Compstatin, Journal of Immunology 165:2491-2499. DOI: 10.4049/​jimmunol.165.5.2491.
84. Klepeis JL, Floudas CA, Morikis D, Lambris JD (1999) Predicting peptide structures using NMR data and deterministic global optimization, Journal of Computational Chemistry 20:1354-1370.  DOI: 10.1002/(SICI)1096-987X(199910)20:13<1354::AID-JCC3>3.0.CO;2-N.
85. Newlon MG, Roy M, Morikis D, Hausken ZE, Coghlan V, Scott JD, Jennings PA (1999) The molecular basis for protein kinase A anchoring revealed by solution NMR, Nature, Structural Biology 6:222-227. DOI:10.1038/6663.
86. Morikis D, Assa-Munt N, Sahu A, Lambris JD (1998) Solution structure of compstatin, a potent complement inhibitor, Protein Science 7:619-627. DOI: 10.1002/pro.5560070311. SI.   
87. Morikis D, Wright PE (1996) Hydrogen exchange in the carbon monoxide complex of soybean leghemoglobin, European Journal of Biochemistry 237:212-220. DOI: 10.1111/j.1432-1033.1996.0212n.x.
88. Brüschweiler R, Morikis D, Wright PE (1995) Hydration of the partially folded peptide RN 24 studied by multidimensional NMR, Journal of Biomolecular NMR 5:353-356. DOI: 10.1007/BF00182277.
89. Morikis D, Lepre CA, Wright PE (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. DOI: 10.1111/j.1432-1033.1994.tb19977.x.
90. Merutka G, Morikis D, Brüschweiler R, Wright PE (1993) NMR evidence for multiple conformations in a highly helical model peptide, Biochemistry 32:13089-13097. DOI: 10.1021/bi00211a019.
91. Morikis D, Brüschweiler R, Wright PE (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. DOI: 10.1021/ja00067a700.
92. Sage JT, Morikis D, Li P, Champion PM (1992) Low pH myoglobin photoproducts, Biophysical Journal 61:1041-1044. DOI: https://doi.org/10.1016/S0006-3495(92)81912-4.
93. Zhu L, Sage JT, Rigos AA, Morikis D, Champion PM (1992) Conformational interconversion in protein crystals, Journal of Molecular Biology 224:207-215. DOI:10.1016/0022-2836(92)90584-7.
94. Wells AV, Sage JT, Morikis D, Champion PM, Chiu ML, Sligar SG (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. DOI: 10.1021/ja00025a034.
95. Morikis D, Li P, Bangcharoenpaurpong O, Sage JT, Champion PM (1991) Resonance Raman scattering as a probe of electron nuclear coupling: Applications to heme proteins, Journal of Physical Chemistry 95:3391-3398. DOI: 10.1021/j100161a077.
96. Sage JT, Morikis D, Champion PM (1991) Spectroscopic studies of myoglobin at low pH: Heme structure and ligation, Biochemistry 30:1227-1237. DOI: 10.1021/bi00219a010.
97. Egeberg KD, Springer BA, Martinis SA, Sligar SG, Morikis D, Champion PM (1990) Alteration of sperm whale myoglobin heme axial ligation by site directed mutagenesis, Biochemistry 29:9783-9791. DOI: 10.1021/bi00494a004.
98. Morikis D, Champion PM, Springer BA, Egeberg KD, Sligar SG (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.
99. Morikis D, Champion PM, Springer BA, Sligar SG (1989) Resonance Raman investigations of site directed mutants of myoglobin: Effects of distal histidine replacement, Biochemistry 28:4791-4800. DOI: 10.1021/bi00437a041.
100. Sage JT, Morikis D, Champion PM (1989) Resonance Raman studies of oriented chromophores: Metmyoglobin single crystals, Journal of Chemical Physics 90:3015-3032. DOI: http://dx.doi.org/10.1063/1.455904.
101. Morikis D, Sage JT, Rizos AK, Champion PM (1988) Resonance Raman studies of myoglobin single crystals, Journal of the American Chemical Society 110:6341-6342. DOI: 10.1021/ja00227a011.
102. Sligar SG, Egeberg KD, Sage JT, Morikis D, Champion PM (1987) Alteration of heme axial ligands by site directed mutagenesis: A cyhrome becomes a catalytic demethylase, Journal of the American Chemical Society 109:7896-7897. DOI: 10.1021/ja00259a056.

1. Ojha H, Panwar HS, Gorham RD Jr, Morikis D, Sahu A (2014) Viral regulators of complement activation: structure, function and evolution, Molecular Immunology 61:89-99. DOI: 10.1016/j.molimm.2014.06.004. 
2. Kieslich CA, Tamamis P, Gorham Jr RD, López de Victoria A, Sausman N, Archontis G, Morikis D (2012) Exploring protein-ligand and protein-protein interactions in the immune system using molecular dynamics and continuum electrostatics, Current Physical Chemistry 2:324-343. DOI: 10.2174/1877946811202040324.
3. Gorham Jr RD, Kieslich CA, Morikis D (2011) Electrostatic clustering and free energy calculations provide a foundation for protein design and optimization, Annals of Biomedical Engineering 39:1252-1263. DOI: 10.1007/s10439-010-0226-9.
4. Mallik B, Morikis D (2006) Applications of molecular dynamics simulations in immunology: a useful computational method in aiding vaccine design, Current Proteomics 3:259-270. DOI: 10.2174/157016406780655568.
5. Morikis D, Mallik B, 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.
6. Wu J, Morikis D (2006) Molecular thermodynamics for charged biomacromolecules, Fluid Phase Equilibria 241:317-333.  Special Festschrift issue in honor of Professor John M. Prausnitz. DOI: 10.1016/j.fluid.2005.12.044.           
7. Morikis D, Lambris JD (2004) Physical methods for structure, dynamics, and binding in immunological research, Trends in Immunology 25:700-707.  Special anniversary issue for the 25th year birthday of Immunology Today/Trends in Immunology.  DOI: 10.1016/j.it.2004.09.009.
8. Holland MCH, Morikis D, Lambris JD (2004) Synthetic small molecule complement inhibitors, Current Opinion in Investigational Drugs 5:1164-1173. Link.
9. Mastellos D, Morikis D, Strey C, Holland MC, Lambris JD (2004) From atoms to systems: a cross-disciplinary approach to complement mediated functions, Molecular Immunology 41:153-164. DOI: 10.1016/j.molimm.2004.03.016.
10. Morikis D, Soulika AM, Mallik B, Klepeis JL, Floudas CA, Lambris JD (2004) Improvement of the anti-C3 activity of compstatin using rational and combinatorial approaches, Biochemical Society Transactions 32:28-32. DOI: 10.1042/bst0320028.
11. Mastellos D, Morikis D, Isaacs SN, Holland MC, Strey CW, Lambris JD (2003) Complement: structure, functions, evolution, and viral molecular mimicry, Immunologic Research 27:367-386.  DOI: 10.1385/IR:27:2-3:367. 
12. Morikis D, Lambris JD (2002) Structural aspects and design of low-molecular-mass complement inhibitors, Biochemical Society Transactions 30:1026-1036. DOI: 10.1042/bst0301026. 

Morikis D, Lambris JD (Eds.) (2005) Structural Biology of the Complement System, CRC Press/Taylor & Francis Group, Boca Raton, FL (ISBN 0-8247-2540-9). 370 pages. Link. Reviews: by Tsokos G (2005) Clinical Immunology 116:306. Link; by Gordon D (2006) Immunology and Cell Biology 84:486. Link; by Martinez OP (2006) World Allergy Organization, News & Notes. Link; by Cohen MC (Dries, DJ, Ed.) (2007) Shock 27:343. Link; by Bunko K, Kennedy JF (2008) International Journal of Biological Macromolecules 42:400-401. Link. 

1. Floudas CA, Fung HK, Morikis D, Taylor MS, 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, pp 133-184, RP Mondaini, PM Pardalos (Eds.), Springer, New York. DOI: 10.1007/978-3-540-76784-8_4.
2. Morikis D, Floudas CA, Lambris JD (2005) Structure-based integrative computational and experimental approach for the optimization of drug design, in ICCS 2005, Lecture Notes in Computer Science: Computational Science, pp 680-688, VS Sunderam, GD van Albada, PMA Sloot, JJ Dongarra (Eds.), Springer-Verlag, Berlin-Heidelberg. DOI: 10.1007/b136571.
3. Morikis D, Lambris JD (2005) Structure, dynamics, activity, and function of compstatin and design of more potent analogs, in Structural Biology of the Complement System, pp 317-340, D Morikis, JD Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL.  Link.
4. Morikis D, Holland MCH, Lambris JD (2005) Structure of the anaphylatoxins C3a and C5a, in Structural Biology of the Complement System, pp 161-177, D Morikis, JD Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL.  Link.
5. Morikis D, Lambris JD (2005), The building blocks of the complement system, in Structural Biology of the Complement System, pp 1-18, D Morikis, JD Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL.  Link.
6. Sahu A, Morikis D, Lambris JD (2000) Complement inhibitors targeting C3, C4, and C5, in Contemporary Immunology: Therapeutic Interventions in the Complement System, pp 75-112, JD Lambris, VM Holers (Eds.), Humana Press Inc., Totowa, New Jersey. DOI: 10.1007/978-1-59259-017-9.
7. Morikis D, Newlon MG, Jennings PA (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, pp 141-156, CA Floudas, PM Pardalos (Eds.), Nonconvex Optimization and its Applications vol 40, Kluwer Academic Publishers, Dordrecht, the Netherlands. DOI: 10.1007/978-1-4757-3218-4.
8. Morikis D, Sahu A, Moore WT, Lambris JD (1999) Design, structure, function and application of compstatin, in Bioactive Peptides in Drug Discovery and Design: Medical Aspects, pp 235-246, J Matsoukas, T Mavromoustakos (Eds.), Biomedical and Health Series, Ios Press, Amsterdam, the Netherlands.  Link.

PhD Dissertations

1. Mohan RR (2018) Mapping the Druggability of Complement C3 and its Derivatives, and Inhibitor Design. PhD in Bioengineering, University of California, Riverside. Link.
2. Harrison RES (2018) Multi-Scale Design of Surveillance and Regulation Within the Complement System. PhD in Bioengineering, University of California, Riverside. Link.
3. Gaieb Z (2016) Molecular Switches Coordinate Dynamically Coupled Allosteric Networks in Protein Complexes. PhD in Bioengineering, University of California, Riverside. Link.
4. Gorham RD Jr (2013) Mechanistic Exploration of Complement System Interactions and Design of Complement-Targeted Therapeutics. PhD in Bioengineering, University of California, Riverside. Link.
5. Kieslich CA (2012) Development and Applications of a Computational Framework for Protein and Drug Design. PhD in Bioengineering, University of California, Riverside. Link.
6. López de Victoria A (2012) Studies of Protein Interactions and Knowledge-Based Drug Design: (A) The Electrostatic Nature of Recognition Between HIV-1 gp120 V3 Loop and Coreceptors CCR5/CXCR4, (B) Complement System Inhibition by Compstatin Family Peptides. PhD in Bioengineering, University of California, Riverside. Link.
7. Hakkoymaz H (2010) Clustering Techniques for Data Mining and Protein Design Around the Concept of Locality. PhD in Computer Science, University of California, Riverside. Link.
8. Zhang L (2007) Studies of Immunophysical Properties of the Complement System using Molecular Dynamics and Electrostatics. PhD in Chemistry, University of California, Riverside. Link.
9. Morikis D (1990) Resonance Raman Investigations of Heme Proteins in the Liquid, Frozen and Crystalline Phase: a Study of the Heme Pocket of Myoglobin. PhD in Physics, Northeastern University, Boston, MA. 456 pages. Link.

MS Theses/Projects

1. Hlava D (2012) Insights into Toxin Binding to Tubulin as a Possible Trigger in Parkinson’s Disease Using Molecular Modeling. MS in Bioengineering, University of California, Riverside. Link.
2. Yang J (2006) Implementation of a high-throughput computational protocol for calculation and clustering of electrostatic potentials of protein families. MS in Computer Science, University of California, Riverside.

1. Tamamis P, López de Victoria A, Gorham RD Jr, Bellows-Peterson ML, Floudas CA, Morikis D, Archontis G (2012) Iterative computational and experimental drug design studies of the complement inhibitor compstatin, in From Computational Biophysics to Systems Biology (CBSB11) – Celebrating Harold Scheraga’s 90th Birthday, P Carloni, UHE Hansmann, T Lippert, JH Meinke, S Mohanty, W Nadler, O Zimmermann (Eds.), John von Neumann Institute für Computing, NIC Series, Vol. 40, p.p. 209-212. Conference, 7/20-22/2011, Jülich, Germany.
2. Morikis D, Mallik B, 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), pp 80-85. Proceedings of the conference held in Vouliagmeni, Athens, Greece, 7/14-16/2006.
3. Floudas CA, Klepeis JL, Lambris JD, 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, CA Floudas, R Agrawal (Eds.), CACHE Corporation, Austin TX. Proceedings of the Conference held at Princeton University, Princeton, NJ, 7/11-16/2004.
4. Champion PM,Morikis D, Li P, Sage JT (1990) Resonance Raman investigations of native and mutant myoglobins, in Proceedings of the XII International Conference on Raman Spectroscopy (ICORS), pp 664‑665, JR Durig, JF Sullivan (Eds.), John Wiley and Sons Inc. Proceedings of the Conference held at Columbia, SC, 9/13-17/1990.
5. Champion PM, Morikis D, Springer B, Sligar SG (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, RJH Clark, DA Long (Eds.), John Wiley and Sons Inc. Proceedings of the Conference held at London, UK, 9/5‑9/1988.

1. Morikis D (2005) CD accompanying the book Structural Biology of the Complement System, CRC Press/Taylor & Francis Group, Boca Raton, FL.  Link.
2. Morikis D (2002) UCR Biomolecular Modeling Workshop: hands-on tutorial on structural modeling. Link.

1. Winicki NM, Harrison RES, Perry JP, Morikis D (2018) Identification of Targetable Surfaces of Cks1 for Development of New Cancer Therapeutics, UCR Undergraduate Research Journal XII:111-119. Link
2. Sai S, Mohan RR, Nair MG, Morikis D (2017) In Silico Physicochemical Analysis of Helical Interactions in Resistin, UCR Undergraduate Research Journal XI:43-49. Link
3. Muk S, Gorham RD Jr, Morikis D (2015) Regulation of complement activation through factor D inhibition: a drug discovery study, UCR Undergraduate Research Journal IX:85-90. Link
4. Zewde N, Dorado A, Gorham RD Jr, Morikis D (2014) Quantitative modeling of the alternative pathway in complement immune system, UCR Undergraduate Research Journal VIII:75-82. Link
5. Lederman I, Morikis D (2014) Network analysis of intra-molecular interactions of the HIV-1 gp120 V3 loop, UCR Undergraduate Research Journal VIII:25-32. Link
6. Baddour B, Gorham, RD Jr, Morikis D (2014) Electrostatic analysis of complement factor D, UCR Undergraduate Research Journal VIII:5-12. Link
7. Rodriguez W, Gorham RD Jr, Kieslich C, López de Victoria A, Morikis D (2012) Molecular analysis of the interaction between Staphylococcus aureus protein Sbi and immune system protein C3d, UCR Undergraduate Research Journal VI:23-29. Link
8. Nichols A, Morikis D, Gorham RD Jr (2011) Physicochemical analysis of the interaction between Epstein-Barr virus glycoprotein gp350 and complement receptor 2 using AESOP (Analysis of Electrostatic Similarities Of Proteins), UCR Undergraduate Research Journal V:37-43. Link
9. Foronda MK, López de Victoria A, Morikis D (2010) Electrostatic exploration of membrane cofactor protein (MCP) using computational alanine scans, Poisson-Boltzmann electrostatics and experimental mutagenesis data, UCR Undergraduate Research Journal IV:59 (17 pages).Link
10. Desai M, Goodman GN, Morikis D (2010) Electrostatic properties of decay-accelerating factor (DAF), UCR Undergraduate Research Journal IV:11-17. Link
11. Vazquez H, Goodman G, López de Victoria A, Kieslich C, Morikis D (2009) The role of electrostatics in the function of Factor H, and its relation to complement system-mediated disease, UCR Undergraduate Research Journal III:49-56. Link
12. Cheung AS, Yang J, Kieslich CA, Morikis D (2008) Computational prediction of association free energies for the C3d-CR2 complex and comparison to experimental data, UCR Undergraduate Research Journal II:13-22. Link
13. 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.

• 180 conference abstracts, available upon request.

• 31 Faculty of 1000 – Biology recommendations (http://f1000biology.com/).

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

1. Morikis D (1982) Introduction to color photography, Thessaloniki, Greece (text for general audience, in Greek). 34 pages.
2. Morikis D (1985-) Various software packages for data analysis and simulations.