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Diana Roe, Ph.D. |
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My research focuses on the problem of molecular recognition, or
how two molecules "recognize" and bind to each other. This
provides the fundamental basis for understanding important
biological processes such as how a protein binds to its receptor,
how an antibody interacts with and antigen, or how a drug molecule
interacts with its target protein. I work in "structure-based"
design, meaning I start with a three dimensional structure of two
molecules, and use molecular mechanics/dynamics and docking codes
as tools to predict their interactions.
I both develop and apply new software tools for structure based molecular design. I developed the BUILDER program for de novo drug design, and CombiBUILD for applying structure-based design to combinatorial chemistry libraries. My current applications are in the area of protein toxins. I'm searching for small molecules that block the function of toxins, and thus are potential lead drug compounds (antitoxins). I'm also looking for small molecules that bind selectively to a protein toxin that can be useful for affinity-based sensors. |
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Recent Publications Zhou, CLE; Zemla, AT; Roe, D; Young, M; Lam, M; Schoeniger, JS; Balhorn, R. "Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin." Bioinformatics, (2005), 21(14), 3089-3096 PubMed Wang, G; De, J; Schoeniger, JS; Roe, DC; Carbonell, RG. "A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin B: isolation from a solid phase combinatorial library." Journal of Peptide Research, (2004), 64(2), 51-64. PubMed Cosman, M; Lightstone, FC; Krishnan, VV; Zeller, L; Prieto, MC; Roe, DC; Balhorn, R. "Identification of novel small molecules that bind to two different sites on the surface of tetanus toxin C fragment." Chemical Research in Toxicology; (2002), 15(10), 1218-1228.
Lightstone FC, Prieto MC, Singh AK, Piqueras MC, Whittal RM, Knapp MS, Balhorn R, Roe DC.
"Identification of novel small molecule ligands that bind to tetanus toxin."
Chem Res Toxicol 13(5):356-62. 2000.
Kick EK, Roe DC, Skillman AG, Liu G, Ewing TJ, Sun Y, Kuntz ID, Ellman JA.
"Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin
D." Chem Biol 4(4):297-307. 1997.
Roe DC, Kuntz ID. "BUILDER v.2: improving the chemistry of a de novo design strategy."
J Comput Aided Mol Des 9(3):269-82. 1995.
Grootenhuis PD, Roe DC, Kollman PA, Kuntz ID. "Finding potential DNA-binding
compounds by using molecular shape." J Comput Aided Mol Des 8(6):731-50. 1994.
Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID.
"Automated site-directed drug design using molecular lattices."
J Mol Graph 10(2):66-78, 106. 1992.
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Contact Information
Dr. Diana Roe
dcroe@sandia.gov |
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