Publications

• Naughton KL, Phan L, Leung EM, Kautz R, Lin Q, Van Dyke Y, Marmiroli B, Sartori B, Arvai A, Li S, Pique ME, Naeim M, Kerr JP, Aquino MJ, Roberts VA, Getzoff ED, Zhu C, Bernstorff S, Gorodetsky AA, (2016)Adv. Mater., 28, 8405-8412.
• Hehle,V. K., Paul, M. J., Roberts, V. A., van Dolleweerd, C. J., and Ma, J. K-C., (2016) "Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants", FASEB J., 30, 1590-1598.
• Roberts, V. A., (2015) "C-terminal domain of integrase binds between the two active sites", J. Chem. Theory Comput., 11, 4500-4511.
• Roberts, V. A., Pique, M. E., Ten Eyck, L. F., Li, S., (2013) "Predicting protein-DNA interactions by full search computational docking", Proteins, 81, 2106-2118.
• Roberts, V. A., Thompson, E. E., Pique, M. E., Perez, M. S., Ten Eyck, L. F., (2013) "DOT2: Macromolecular Docking With Improved Biophysical Models", J. Comput. Chem., 34, 1743-1758.
• Roberts, V. A., Pique, M. E., Hsu, S., Li, S., Slupphaug, G., Rambo, R. P., Jamison, J. W., Liu, T., Lee, J. H., Tainer, J. A., Ten Eyck, L. F., Woods, V. L. Jr., (2012) "Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase", Nuc. Acids. Res., 40, 6070-6081.
• Trinh, M.-H., Odorico, M., Pique, M. E., Teulon, J.-M., Roberts, V. A., Ten Eyck, L. F., Getzoff, E. D., Parot, P., Chen, S.-w. W., Pellequer, J.-L., (2012) "Computational reconstruction of multidomain proteins using atomic force microscopy data", Structure, 20, 113-120.
• Noodleman, L., Pique, M. E., Roberts, V. A., (2009) "Properties and Functions of Iron-Sulfur Clusters", In Wiley Encyclopedia of Chemical Biology, Begley, T. P. (Ed.) John Wiley and Sons, New York.
• Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A., (2008) "XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations", Cell, 133, 789-800.
• Fan, L. and Roberts, V. A., (2006) "Complex of Linker Histone H5 with the Nucleosome and Its Implications for Chromatin Packing", Proc. Natl. Acad. Sci. USA, 103, 8384-8389.
• Pellequer, J.-L., Chen, S.-W. W., Keum, Y.-S., Karu, A. E., Li, Q. X., and Roberts, V. A., (2005) "Structural Basis for Preferential Binding of Non-Ortho-Substituted Polychlorinated Biphenyls by the S2B1 Antibody", J. Mol. Recog., 18, 282--294.
• Chakravarthy, S., Bao Y., Roberts V. A., Tremethick D., Luger K. (2004) "Structural Characterization of Histone H2A Variants", Cold Spring Harbor Symp. Quant. Biol., 69, 1-8.
• Roberts, V. A., Case, D. A., and Tsui, V., (2004) "Predicting Interactions of Winged-Helix Transcription Factors with DNA", Proteins, 57, 172-187.
• Adesokan, A. A., Roberts, V. A., Lee, K. W., Lins, R. D., and Briggs, J. M., (2003) "Prediction of HIV-1 Integrase/Viral DNA Interactions in the Catalytic Domain by Fast Molecular Docking" J. Med. Chem., 47, 821-828.
• Law, D. S., Ten Eyck, L. F., Katzenelson, O., Tsigelny, I., Roberts, V. A., Pique, M. E., and Mitchell, J. C., (2003) "Finding Needles in Haystacks: Reranking DOT Results by Using Shape Complementarity, Cluster Analysis and Biological Information", Proteins, 52, 33-40.
• Brudler, R., Hitomi, K., Daiyasu, H., Toh, H., Kucho, K., Ishiura, M., Kanehisa, M., Roberts, V. A., Todo, T., Tainer, J. A., and Getzoff, E. D., (2003) "Identification of a New Crytochrome Class: Structure, Function, and Evolution", Mol. Cell, 11, 1-20.
• Castagnetto, J. M., Hennessy, S. W., Roberts, V. A., Getzoff, E. D., Tainer, J. A., and Pique, M. E., (2002) "MDB: The Metalloprotein Database and Browser at The Scripps Research Institute", Nuc. Acids Res., 30, 379-382.
• Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi, V., Mitchell, J. C., Nelson, E., Tsigelny, I., and Ten Eyck, L. F., (2001) "Protein Docking Using Continuum Electrostatics and Geometric Fit", Prot. Eng., 14, 105-113.
• Pellequer, J.-L., Chen, S.-w. W., Bell, C. W., Feeney, A., Karu, A. E., Li, K., Li, Q. X., and Roberts, V. A., (2000) "Architecture of Antibody Binding Sites for Polynuclear Aromatic Hydrocarbons", In Nuclear Site Remediation, (Eller, P. G. and Heineman, W. R., eds.), pp. 398-416, American Chemical Society, Washington, D. C.
• Pellequer, J.-L., Zhao, B., Kao, H.-I., Bell, C. W., Li, K., Li, Q. X., Karu, A. E., and Roberts, V. A., (2000) "Stabilization of Bound Polycyclic Aromatic Hydrocarbons by a pi-Cation Interaction ", J. Mol. Biol., 302, 691-699.
• Smithrud, D. B., Benkovic, P. A., Benkovic, S. J., Roberts, V. A., Liu, J., Iwama, S., Phillips, B. W., Neagu, I., Smith, A. B., III, Hirschmann, R., (2000) "Cyclic Peptide Formation Catalyzed by an Antibody Ligase", Proc. Natl. Acad. Sci, USA, 97, 1953-1958.
• Roberts, V. A. and Pique, M. E., (1999) "Definition of the Interaction Domain for Cytochrome c on Cytochrome c Oxidase: III. Prediction of the Docked Complex by a Complete, Systematic Search", J. Biol. Chem., 274, 38051--38060.
• Pellequer, J.-L., Chen, S. W., Roberts, V. A., Tainer, J. A., and Getzoff, E. D., (1999) "Unravelling the Effect of Changes in Conformation and Compactness at the Antibody VL-VH Interface Upon Antigen Binding", J. Mol. Recog., 12, 267--275.
• Thayer, M. M., Olender, E. H., Arvai, A. S., Koike, C. K., Canestrelli, I. L., Stewart, J. D., Benkovic, S. J., Getzoff, E. D., and Roberts, V. A., (1999) "Structural Basis for Amide Hydrolysis Catalyzed by the 43C9 Antibody", J. Mol. Biol., 291, 329--345.
• Jung, Y.-S., Roberts, V. A., Stout, C. D., and Burgess, B. K., (1998) "Complex Formation between Azotobacter vinelandii Ferrodoxin I and Its Physiological Electron Donor NADPH-Ferredoxin Reductase", J. Biol. Chem., 274, 2978-2987.
• Li, K., Chen, R., Zhao, B., Liu, M., Karu, A. E., Roberts, V. A., and Li, Q. X., (1998) "Monoclonal Antibody-based ELISAs for Part-per-billion Determination of Polycyclic Aromatic Hydrocarbons: Effects of Haptens and Formats on Sensitivity and Specificity", Anal. Chem., 71, 302-309.
• Wiens, G. D., Roberts, V. A., Whitcomb, E. A., O'Hare, T. O., Stenzel-Poore, M. P., and Rittenberg, M. B., (1998) "Harmful Somatic Mutations: Lessons From the Dark Side", Immunol. Rev., 162, 197-209.
• Nachman, R. J., Roberts, V. A., Lange, A. B., Orchard, I., Holman, G.M., and Teal, E. A., (1997) "Active Conformation and Mimetic Analog Development for the Pyrokinin-PBAN-Diapause-Pupariation and Myosuppressin Insect Neuropeptide Families", in Phytochemicals for Pest Control, Hedin, P. A., Hollingworth, R. M., Masler, E. P., Miyamoto, J. and Thompson, D. G., eds., American Chemical Society, Washington, D. C., 277-291.
• Roberts, V. A., Nachman, R. J., Coast, G. M., Hariharan, M., Chung, J. S., Holman, G. M., and Tainer, J. A., (1997) "Consensus Chemistry and beta-Turn Conformation of the Active Core of the Insect Kinin Neuropeptide Family", Chemistry & Biology, 4, 105-117.
• Nachman, R.J., Olender, E.H., Roberts, V.A., Holman, G.M., and Yamamoto, D., (1996) "A Nonpeptidal Peptidomimetic Agonist of the Insect FLRFamide Myosuppressin Family", Peptides, 17, 313-320.
• Brown, M., Rittenberg, M. B., Chen, C., and Roberts, V. A., (1996) "Tolerance to Single, but Not Multiple, Amino Acid Replacements in Antibody V_H CDR2: A Means of Minimizing B Cell Wastage from Somatic Hypermutation", J. Immunol., 156, 3285-3291.
• Pulito, V. L., Roberts, V. A., Adair, J. R., Rothermel, A. L., Collins, A. M., Varga, S. S., Martocello, C., Bodmer, M., Jolliffe, L. K., and Zivin, R. A., (1996) "Humanization and Molecular Modeling of the Anti-CD4 Monoclonal Antibody, OKT4A", J. Immunol., 156, 2840-2850.
• Ten Eyck, L. F., Mandell, J., Roberts, V. A., and Pique, M. E., (1995) "Surveying Molecular Interactions With DOT", in Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego, IEEE Computer Society Press, Los Alamitos, California. available at the URL http://www.supercomp.org/sc95/proceedings/636_LTEN/SC95.HTM.
• Nachman, R. J., Roberts, V. A., Holman, G. M., and Beier, R. C., (1995) "Pseudodipeptide Analogs of the Pyrokinin/PBAN (FXPRLa) Insect Neuropeptide Family Containing Carbocyclic Pro-Mimetic Conformational Components", Reg. Pep., 57, 359-370.
• Chen, C., Roberts, V. A., Stevens, S., Brown, M., Stenzel-Poore, M. P., and Rittenberg, M. B., (1995) "Enhancement and Destruction of Antibody Function by Somatic Mutation: Unequal Occurrence is Controlled by V Gene Combinatorial Associations", EMBO J., 14, 2784-2794.
• Roberts, V. A., Stewart, J. D., Crowder, M. W., Benkovic, S. J., and Getzoff, E. D., (1995) "Probing Catalytic Mechanism and Designing Metal-Binding Sites in a Catalytic Antibody by Computer Modelling and Site-Directed Mutagenesis", in Perspectives on Protein Engineering & Complementary Technologies - 1995, Geisow, M. J. and Epton, R., eds., Mayflower Worldwide Ltd., Birmingham, England, 184-188.
• Crowder, M. W., Stewart, J. D., Roberts, V. A., Bender, C. J., Tevelrakh, E., Peisach, J., Getzoff, E. D., Gaffney, B. J., and Benkovic, S. J., (1995) "Spectroscopic Studies on the Designed Metal-Binding Sites of the 43C9 Single Chain Antibody", J. Amer. Chem. Soc., 117, 5627-5634.
• Bell, C. W., Roberts, V. A., Scholthof, K.-B. G., Zhang, G., and Karu, A. E., (1995) "Recombinant Antibodies to Diuron: A Model for the Phenylurea Combining Site", in Immunoanalysis of Agrochemicals, Emerging Technologies, Nelson, J. O., Karu, A. E., and Wong, R. B., eds., American Chemical Society, Washington D. C., 50-71.
• Roberts, V. A. and Getzoff, E. D., (1995) "Metalloantibody Design", FASEB J., 9, 94-100.
• Israels, R., Gersappe, D., Fasolka, M., Roberts, V. A., and Balazs, A. C., (1994) "pH-Controlled Gating in Polymer Brushes", Macromolecules, 27, 6679-6682.
• Friedman, A. R., Roberts, V. A., and Tainer, J. A., (1994) "Predicting Molecular Interactions and Inducible Complementarity: Fragment Docking of Fab-Peptide Complexes", Proteins, 20, 15-24.
• Stewart, J. D., Roberts, V. A., Thomas, N. R., Getzoff, E. D., and Benkovic, S. J., (1994) "Site-Directed Mutagenesis of Catalytic Antibody: An Arginine and a Histidine Residue Play Key Roles", Biochemistry, 33, 1994-2003.
• Stewart, J. D., Roberts, V. A., Crowder, M. W., Getzoff, E. D., and Benkovic, S. J., (1994) "Creation of a Novel Biosensor for Zn(II)", J. Amer. Chem. Soc., 116, 415-416.
• Roberts, V. A., Stewart, J. D., Benkovic, S. J., and Getzoff, E. D., (1994) "Catalytic Antibody Model and Mutagenesis Implicate Arginine in Transition-State Stabilization", J. Mol. Biol., 235, 1098-1116.
• Nachman, R. J., Kuniyoshi, H., Roberts, V. A., Holman, G. M., and Suzuki, A., (1993) "Active Conformation of the Pyrokinin/PBAN Neuropeptide Family for Pheromone Biosynthesis in the Silkmoth Bombyx mori", Biochem. Biophys. Res. Comm., 193, 661-666.
• Roberts, V. A., (1993), "Computer-Aided Molecular Design", in 1994 Yearbook of Science and the Future, Calhoun, D., ed., Encyclopaedia Britannica, 86-103.
• Roberts, V. A., Getzoff, E. D., and Tainer, J. A., (1992), "Structural Basis of Antigenic Cross-Reactivity", in Structure of Antigens: Volume II, Van Regenmortel, M. H. V., ed., The Telford Press, Chapter 2, 31-54.
• Chen, C., Roberts, V. A., and Rittenberg, M. B., (1992), "Generation and Analysis of Random Point Mutations in an Antibody CDR2 Sequence: Many Mutated Antibodies Lose Their Ability to Bind Antigen", J. Exp. Med., 176, 855-866.
• Tainer, J. A., Roberts, V. A., and Getzoff, E. D., (1992), "Protein Metal-Binding Sites", Cur. Opin. Biotech., 3, 378-387.
• Tainer, J. A., Roberts, V. A., and Getzoff, E. D., (1991), "Metal Binding Sites in Proteins", Cur. Opin. Biotech., 2, 582-591.
• Roberts, V. A., Freeman, H. C., Olson, A. J., Tainer, J. A., and Getzoff, E. D., (1991), "Electrostatic Orientation of the Electron-Transfer Complex Between Plastocyanin and Cytochrome c", J. Biol. Chem., 266, 13431-13441.
• Nachman, R. J., Roberts, V. A., Dyson, H. J., Holman, G. M., and Tainer, J. A., (1991), "The Active Conformation of an Insect Neuropeptide Family", Proc. Natl. Acad. Sci. USA, 88, 4518-4522.
• Fisher, C. L., Roberts, V. A., and Hagler, A. T., (1991), "The Influence of Environment on the Antifolate Drug Trimethoprim. Energy Minimization Studies", Biochemistry, 30, 3518-3526.
• Fisher, C. L., Hallewell, R. A., Roberts, V. A., Tainer, J. A., and Getzoff, E. D., (1990), "Probing the Structural Basis for Enzyme-Substrate Recognition in Cu, Zn Superoxide Dismutase", Free Rad. Res. Commun., 12-13, 287-296.
• Roberts, V. A., Fisher, C. L., Redford, S. M., McRee, D. E., Parge, H. E., Getzoff, E. D., and Tainer, J. A., (1990), "Mechanism and Atomic Structure of Superoxide Dismutase", Free Rad. Res. Commun., 12-13, 269-278.
• Tainer, J. A. and Roberts, V. A., (1990), "Enzyme Motifs in Antibodies", Nature (Scientific Correspondence), 348, 589.
• Tainer, J. A., Roberts, V. A., Fisher, C. L., Hallewell, R. A., and Getzoff, E. D., (1990), "Mechanism and Structure of Superoxide Dismutases", in A Study of Enzymes. Volume II. Mechanism of Enzyme Action, S. A. Kuby, ed., CRC Press, 499-538.
• Nachman, R. J., Roberts, V. A., Holman, G. M., and Tainer, J. A., (1990), "Consensus Chemistry and Conformation of an Insect Neuropeptide", Prog. Comp. Endocrinol., 342, 60-66.
• Tainer, J. A., Deal, C. D., Geysen, H. M., Roberts, V. A., and Getzoff, E. D., (1990), "Defining Antibody-Antigen Recognition: Towards Engineered Antibodies and Epitopes", Intern. Rev, Immunol., 7, 165-188.
• Iverson, B. L., Iverson, S. A., Roberts, V. A., Getzoff, E. D., Tainer, J. A., Benkovic, S. J., and Lerner, R. A., (1990), "Metalloantibodies", Science, 249, 659-662.
• Roberts, V. A., Iverson, B. L., Iverson, S. A., Benkovic, S. J., Lerner, R. A., Getzoff, E. D., and Tainer, J. A., (1990), "Antibody Remodeling: A General Solution to the Design of a Metal-Coordination Site in an Antibody Binding Pocket", Proc. Natl. Acad. Sci. USA, 87, 6654-6658.
• Behar, S. M., Chien, N. C., Corbet, S., Diamond, B., Getzoff, E. D., Lustgarten, D., Roberts, V. A., Scharff, M. D., and Shin, S.-U., (1989), "Impact of Somatic Mutation on the S107(T15) Heavy-Chain V Region of Antibodies Reactive with Self and Nonself", Cold Spring Harbor Symp. Quant. Biol., 54, 921-931.
• Chien, N. C., Roberts, V. A., Giusti, A. M., Scharff, M. D., and Getzoff, E. D., (1989), "Significant Structural and Functional Change of an Antigen Binding Site by a Distant Amino Acid Substitution: Proposal of a Structural Mechanism," Proc. Natl. Acad. Sci. USA, 86, 5532-5536.
• Tainer, J. A., Hallewell, R. A., Roberts, V. A., Parge, H. E., and Getzoff, E. D., (1989), "Probing Enzyme-Substrate Recognition and Catalytic Mechanism in Cu,Zn Superoxide Dismutase," in Oxygen Radicals in Biology and Medicine, Simic, M. G., Taylor, K. A., Ward, J. F., and von Sonntag, C., eds., Plenum Publishing Corporation, pp 635-640.
• Rone, R., Manesis, N., Hassan, M., Goodman, M., Hagler, A. T., Kitson, D., and Roberts, V. A., (1988), "Conformational Analysis of Constrained Dilactam-bridged Tetrapeptides," Tetrahedron, 44, 895-924.
• Dauber-Osguthorpe, P., Roberts, V. A., Osguthorpe, D. J., Wolff, J., Genest, M., and Hagler, A. T., (1988), "Structure and Energetics of Ligand Binding to Proteins: E. coli. Dihydrofolate Reductase-Trimethoprim, A Drug-Receptor System," Proteins: Structure, Function and Genetics, 4, 31-47.
• Roberts, V. A., Dauber-Osguthorpe, P., Osguthorpe, D. J., Levin, E., and Hagler, A. T., (1986), "A Comparison of the Binding of the Ligand Trimethoprim to Bacterial and Vertebrate Dihydrofolate Reductases," Isr. J. Chem., 27, 198-210.
• Roberts, V. A. and Garst, M. E. (1985), "Synthesis of 4-Substituted Cycloheptatrienones by Oxidative Cheleotropic Elimination of Nitrosobenzene from 6-Substituted 8-Phenyl-8-azabicyclo[3.2.1]octa-3,6-dien-1-ones," J. Org. Chem., 50, 893-894.
• Garst, M. E., Roberts, V. A., Houk, K. N. and Rondan, N. G., (1984), "Even Regioselectivity in [6 + 4] Cycloadditions of Unsymmetrical Tropones with Dienes," J. Am. Chem. Soc., 106, 3882-3884.
• Roberts, V. A., Garst, M. E. and Torres, N. E., (1984), "Synthesis of 3-Methoxycycloheptatrienones," J. Org. Chem., 49, 1136-1138.
• Roberts, V. A., (1983), "Cycloaddition Reactions of Substituted Cycloheptatrienones," Ph.D. Thesis, University of California, San Diego, San Diego, California.
• Garst, M. E., Roberts, V. A. and Prussin, C., (1983), "Steric and Electronic Effects of Dienes in Cycloaddition Reactions with Cycloheptatrienone," Tetrahedron, 39, 581-589.
• Garst, M. E., Roberts, V. A. and Prussin, C., (1982), "The Fragmentation of Bicyclo[4.4.1]undecan-11-ones," J. Org. Chem., 47, 3969-3971.
• Garst, M. E. and Roberts, V. A., (1982), "Synthesis of 3- and 4-Carboethoxy-2,4,6-cycloheptatrien-1-one," J. Org. Chem., 47, 2188-2190.