Research    CV    Software    Publications    Talks    Posters

 

 

 
 

Curriculum Vita

 

  

 

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Software

FIRST: Software for Protein Flexibility Analysis

The FIRST ( Floppy Inclusions & Rigid Substructure Topography) software was developed during my doctoral  research as a venture between the research groups of Mike Thorpe and Leslie Kuhn at Michigan State University.  This program may be accessed online at firstweb. and is able to predict the rigid and flexible regions for protein structures in PDB format.

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Publications

10.      A.J. Rader, Daniel H. Vlad, and Ivet Bahar, Maturation Dynamics of Bacteriophage HK97 Capsid, Structure 13, 413-421 (2005). [pdf]

9.      Yongmei Wang, A.J. Rader, Ivet Bahar, and Robert L. Jernigan, Global Ribosome Motions Revealed with Elastic Network Model, Journal of Structural Biology 147(3), 302-314 (2004). [pdf]

8.      A.J. Rader, Gülsüm Anderson, Basak Isin, H. Gobind Khorana, Ivet Bahar and Judith Klein-Seetharaman, Identification of Core Amino Acids Stabilizing Rhodopsin,  Proceedings of the National Academy of Sciences (USA) 101(19), 7246-7251 (2004). [pdf]

7.      A.J. Rader and Ivet Bahar, Folding Core Predictions from Network Models of Proteins, Polymer 45(2),  659-668 (2004). [pdf]

6.      Brandon M. Hespenheide, A.J. Rader, M.F. Thorpe, and Leslie A. Kuhn, Identifying Protein Folding Cores from the Evolution of Flexible Regions during Unfolding, Journal of Molecular Graphics & Modelling 21, 195-207 (2002). [pdf]

5.      A.J. Rader, Brandon M. Hespenheide, L.A. Kuhn, and M.F. Thorpe, Protein Unfolding: Rigidity Lost, Proceedings of the National Academy of Sciences (USA) 99, 3540-3545 (2002). [pdf]

4.      D.J. Jacobs, A.J. Rader, Leslie A. Kuhn, and M.F. Thorpe, Protein Flexibility Predictions Using Graph Theory, PROTEINS: Structure, Function and Genetics 44, 150-165 (2001). [cover figure] [pdf]

3.      M.F. Thorpe, Ming Lei, A.J. Rader, Donald J. Jacobs and Leslie A. Kuhn, Protein Flexibility and Dynamics using Constraint Theory, Journal of Molecular Graphics & Modelling 19, 60-69 (2001). [pdf]

2.      M.F. Thorpe, D.J. Jacobs, N.V. Chubynsky & A.J. Rader, Generic Rigidity of Network Glasses in Rigidity Theory and Applications, Edited by M.F. Thorpe and P.M. Duxbury. Kluwer Academic/Plenum Publishing, New York,  239-277 (1999). [pdf]

1.      D.S. Bracken, K. Kwiatkowski, K.B. Morley, E. Renshaw Foxford, K. Komisarcik, A.J. Rader, & V.E. Viola, Charging Effects in Passivated Silicon Detectors, Nuclear Instruments and Methods in Physics Research A 365, 424-426 (1995). [pdf]

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Invited/Contributed Talks

  • A.J. Rader, "Simulating Viral Capsid Maturation Using Elastic Network Models" Computational Methodology in Modeling Complex Biological Systems Workshop, Pittsburgh Center for Biomedical Computation  Pittsburgh, Pennsylvania, October 13, 2004.

  • A.J. Rader, "Protein Folding Predictions from Network Models" Condensed Matter & Biological Physics Seminar, Department of Physics, Syracuse University, Syracuse, NY, September 24, 2004.

  • A.J. Rader, "Modeling of Bigger Biomolecules & Assemblies" Workshop on Modeling Protein Stability, Flexibility and Motions, Banff, Alberta, Canada, July 17-22, 2004.

  • A.J. Rader, "FIRST and Protein Unfolding" Workshop on Modeling Protein Stability, Flexibility and Motions, Banff, Alberta, Canada, July 17-22, 2004.

  • A.J. Rader, "Perspectives on Protein (un)Folding from Rigidity" American Mathematical Society 2004 Spring Eastern Section Meeting, Rider University, Lawrenceville, NJ, April 17-18, 2004.

  • A.J. Rader, Yongmei Wang, Ivet Bahar, and Robert L. Jernigan, "Motions and Deformations in Ribosome" Biophysical Society 48th Annual Meeting, Baltimore, MD, February 16, 2004.

  • A.J. Rader, "Extensions of FIRST to Nucleotides" Arizona State University, Tempe, AZ, January 30, 2004.

  • A.J. Rader, Gülsüm Anderson, Basak Isin, Judith Klein-Seetharaman, and Ivet Bahar,  "The Folding Core in Rhodopsin" Biological Language Conference, Carnegie Mellon University and University of Pittsburgh, Pittsburgh, PA, November 20-21, 2003.

  • A.J. Rader, "Protein Rigidity and Flexibility: Applications to Folding" 2nd Biological Language Modeling Workshop, Carnegie Mellon University, Pittsburgh, PA, May 14, 2003.

  • A.J. Rader, Brandon M. Hespenheide, Leslie A. Kuhn, M.F. Thorpe, "Protein Unfolding: Rigidity Lost" American Physical Society March Meeting, Austin,TX, March 4, 2003.

  • A.J. Rader, "Protein Rigidity and Flexibility: Applications to Folding and Thermostability" T-10 Theoretical Biology & Biophysics Division, Los Alamos National Laboratory, Los Alamos, NM, October 2002.

  • A.J. Rader, "Protein Rigidity and Flexibility: Applications to Folding and Thermostability" Center for Computational Biology & Bioinformatics, University of Pittsburgh, Pittsburgh, PA, October 2002.

  • A.J. Rader, Protein Unfolding: Rigidity Lost. Condensed Matter Physics Brown Bag Seminar, Department of Physics & Astronomy, Michigan State University, East Lansing, MI, September 27, 2001.

  • A.J. Rader, The Protein Folding Problem. Condensed Matter Physics Brown Bag Seminar, Department of Physics & Astronomy, Michigan State University, East Lansing, MI, October 12, 2000.

  • A.J. Rader, D.J. Jacobs, and M.F. Thorpe, Computational Analysis for Random Bond Model Rigidity Percolation. American Physical Society Centennial Meeting, Atlanta, GA, March 26,1999.

  •  A.J. Rader, K. Kwiatkowski, and V.E. Viola, “Leakage Current Effects in Passivated Silicon Detectors” 5th Annual Argonne Symposium for Undergraduates in Science, Engineering, and Mathematics. Argonne National Laboratory, Argonne, IL, November 4-5, 1994.

     

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Posters

  • A.J. Rader, Gülsüm Anderson, Basak Isin, Judith Klein-Seetharaman, and Ivet Bahar The Folding Core of the G-Protein-Coupled Receptor Rhodopsin Poster at Biophysical Society 48th Annual Meeting, Baltimore, Maryland, February 2004.

  • A.J. Rader and Ivet Bahar Folding Core Predictions from Network Models of Proteins Poster at 35th Central Regional Meeting of the American Chemical Society, Pittsburgh, Pennsylvania,  October 2003.

  • A.J. Rader, Basak Isin, Gülsüm Anderson, Judith Klein-Seetharaman, and Ivet Bahar The Folding Core of the G-Protein-Coupled Receptor Rhodopsin Poster at Science 2003, University of Pittsburgh, Pittsburgh, Pennsylvania, September 2003.

  • A.J. Rader and Ivet Bahar Folding Core Predictions from Network Models of Proteins Poster at UB-SUNY 1st Frontiers in Bioinformatics Symposium, Buffalo, New York, June 2003.

  • A.J. Rader, B.M. Hespenheide, L.A. Kuhn, and M.F. Thorpe, Protein Unfolding Driven by Changing Mean Coordination Poster at the Protein Society Symposium, San Diego, California, August 2002.

  • B.M. Hespenheide, A.J. Rader,  M.F. Thorpe, and L.A. Kuhn, Structural Characterization of Protein Unfolding Pathways  Poster (presented by B.M. Hespenheide) at the Protein Society Symposium, San Diego, California, August 2002.

  • A.J. Rader, B.M. Hespenheide, L.A. Kuhn, and M.F. Thorpe, Protein Unfolding Driven by Changing Mean Coordination Poster at the MSU Center for Biological Modeling Annual Symposium, East Lansing, Michigan, June 2002.

  • B.M. Hespenheide, A.J. Rader,  M.F. Thorpe, and L.A. Kuhn, Structural Characterization of Protein Unfolding Pathways  Poster (presented by B.M. Hespenheide) at the MSU Center for Biological Modeling Annual Symposium, East Lansing, Michigan, June 2002.

  • A.J. Rader, B.M. Hespenheide, L.A. Kuhn, and M.F. Thorpe, The Mean Coordination, <r>, as a Protein Folding Reaction Coordinate Poster at the 16th Annual MSU Center for Fundamental Materials Research Symposium, East Lansing, Michigan, April 2002.

  • B.M. Hespenheide, A.J. Rader,  M.F. Thorpe, and L.A. Kuhn, Protein Folding Cores Identified Using FIRST Flexibility Analysis  Poster (presented by B.M. Hespenheide) at the International Workshop on Protein Folding, Structure and Design, ICTP, Trieste, Italy, June 2001.

  • A.J. Rader, B.M. Hespenheide, L.A. Kuhn, and M.F. Thorpe, Protein Unfolding: Rigidity Lost? Poster at the Center for Biological Modeling Annual Retreat, Augusta, Michigan, May 2001.

  • A.J. Rader, L.A. Kuhn, B.M. Hespenheide and M.F. Thorpe; Protein Unfolding: An Example of a Rigid--Floppy Phase Transition Poster at the 15th Annual CFMR Symposium, MSU, March 26, 2001.

  • A.J. Rader, L.A. Kuhn, B.M. Hespenheide and M.F. Thorpe; The Transition Between Rigidity and Flexibility in Proteins and Glasses Poster at the MSU sponsored Protein Flexibility & Folding Workshop, Traverse City, Michigan, August 13-17, 2000.

  • H. Krishnamurty, A.J. Rader, M.F. Thorpe, L.A. Kuhn, J. G. Zeikus, and C. Vieille; Testing FIRST predictions on protein stability using adenylate kinase as a model enzyme Poster (presented by H. Krishnamurty) at the MSU sponsored Protein Flexibility & Folding Workshop, Traverse City, Michigan, August 13-17, 2000.

  • A.J. Rader, L.A. Kuhn, and M.F. Thorpe; Computational Detection and Analysis of Proteins Flexibility Poster at the 14th Annual CFMR Symposium, MSU, February 2000.

  • A.J. Rader, L.A. Kuhn, and M.F. Thorpe Prediction of Protein Flexibility Poster at LJIS Quantitatvie Challenges in the Post-Genomic Sequence Era: Workshop and Symposium, San Diego, California, January 2000.

  • A.J. Rader and M.F. Thorpe Ligand Binding Effects on Protein Rigidity and Flexibility  Poster at the 47th Annual Midwest Solid State Conference, Ohio University, 1999.

  • A.J. Rader, D.J. Jacobs, M.F. Thorpe, & L.A. Kuhn Rigid and Flexible Regions in Proteins Poster at the 13th Annual CFMR Symposium, MSU, East Lansing, Michigan, 1999.

  • N.V. Chubynsky, A.J. Rader, D.J. Jacobs and M.F. Thorpe Bethe Lattice Model of Rigidity Percolation in Glasses Poster (co-presented with N.V. Chubynsky) at the 46th Annual Midwest Solid State Conference, Iowa State University, Ames, Iowa, 1998 (poster, EPS file compressed in ZIP format, 230 kB)

 

  
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This page written and maintained by A.J. Rader. Last updated on 10/08/04.