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Investigators and Program Directors

image of Alain Laederach

Alain Laederach

Research Scientist, Wadsworth Center,
Computational & Structural Biology
Assistant Professor, School of Public Health, Biomedical Sciences

Ph.D., Iowa State University (2003)
Postdoctoral Fellow, Stanford University,
Genetics Department

E-mail: alain@wadsworth.org
Lab Pages: http://www.wadsworth.org/Laederach/

<< Research Interests

Select Publications

  • Martin, JS, Simmons, K, Laederach, A. Exhaustive. Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding. Algorithms 2009, 2(1), 200-214;
  • Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA. 2009 Feb;15(2):189-99.
  • Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol. 2008 Dec;12(6):655-66.
  • Laederach A.Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. (2008), Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc. 2008;3(9):1395-401.
  • Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A.(2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Research, 2008 Jun;36(11):e63.
  • Das, R., Kudaravalli, M., Jonikas M., Laederach A. Fong R., Schwans, J.P., Baker D., Piccirilli J.A., Altman R.B., and Herschlag, D. (2008) Structural inference of native and partially folded RNA by high-throughput contact mapping PNAS, 105, 4144-4149.
  • Laederach A. (2007) Informatics Challenges in Structured RNA, Briefings in Bioinformatics, 5, 294-303.
  • Laederach A., Shcherbakova, I., Jonikas, M.A., Altman, R.B., Brenowitz, M.(2007) Distinct contribution of electrostatics, initial conformational ensemble and macromolecular stability in RNA folding, PNAS, 104, 7045-50.
  • Laederach A., Chan, J.M., Schwartzman, A., Willgohs, E.S., Altman, R.B. (2007) Co-planar and co-axial orientations of RNA bases and helices, RNA 13, 643-50.
  • Vicens, Q., Gooding A.R., Laederach A., Cech, T.R. (2006) RNA structure mapping in crystals to reveal lattice contacts. RNA 13, 536-48.
  • Russell, R., Das, R., Suh H., Travers, K.J., Laederach A., Engelhardt, M.A., Herschlag D. (2006). The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J. Mol. Biol. 363, 531-544.
  • Laederach A., Shcherbakova, I., Liang, M., Brenowitz, M., Altman, R.B. (2006). Local kinetic measures of macromolecular structure reveal multiple parallel folding pathways for a large RNA molecule. J. Mol.Biol, 358, 1179-1190.
  • Laederach A. Reilly P. J. (2005) Modeling Protein Recognition of Carbohydrates. Proteins, Structure Function and Genetics, 60, 591-597.
  • Das, R., Laederach A. Pearlman, S. M., Herschlag, D, & Altman, R.B. (2005) SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11, 344-354.
  • Liang M.P., Troyanskaya O. G. , Laederach A., Brutlag D.L. & Altman, R.B. (2004) Computational Functional Genomics, IEEE Signal Processing, 21, 62-69.
  • Aikens C.L., Laederach A.& Reilly P. J. (2004) Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking. Proteins 1, 27-35.
  • Allen M.J., Laederach A. Reilly P. J., Mason R.J. & Voelker D.R. (2004) Arg343 in human surfactant protein D governs discrimination between glucose and N-acetylglucosamine ligands. Glycobiology 14, 693-700.
  • Breheny, P., Laederach A., Fulton, D. B. & Andreotti, A. H. (2003). Ligand specificity modulated by prolyl imide bond cis/trans isomerization in the ITK SH2 domain: A quantitative NMR study.J Am Chem Soc 125, 15706-15707.
  • Laederach A., Cradic, K. W., Fulton, D. B. & Andreotti, A. H. (2003). Determinants of intra versus intermolecular self-association within the regulatory domains of Rlk and Itk. J Mol Biol 329, 1011-1020.
  • Laederach A. & Reilly, P. J. (2003). Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comput Chem 24, 1748-1757.
  • Laederach A., Andreotti, A. H. & Fulton, D. B. (2002). Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives. Biochemistry 41, 12359-12368.
  • Laederach A., Cradic, K. W., Brazin, K. N., Zamoon, J., Fulton, D. B., Huang, X. Y. & Andreotti, A. H. (2002). Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: intramolecular contact versus asymmetric homodimerization. Protein Sci 11, 36-45.
  • Allen, M. J., Laederach A., Reilly, P. J. & Mason, R. J. (2001). Polysaccharide recognition by surfactant protein D: novel interactions of a C-type lectin with nonterminal glucosyl residues. Biochemistry 40, 7789-7798.
  • Pletneva, E. V., Laederach A. T., Fulton, D. B. & Kostic, N. M. (2001). The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains. J Am Chem Soc 123, 6232-6245.
  • Rockey, W. M., Laederach A. & Reilly, P. J. (2000). Automated docking of a-(1-->4)- and a-(1-->6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site. Proteins 40, 299-309.
  • Laederach A., Dowd, M. K., Coutinho, P. M. & Reilly, P. J. (1999). Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean b-amylase active site. Proteins 37, 166-175.

Contact Information

E-mail: alain@wadsworth.org .