Zavodszky lab
Publications
Scoring Confidence Index: Statistical Evaluation of Ligand Binding Mode Predictions M.I. Zavodszky, A. Stumpff-Kane, L.J. David, M. Feig, submitted.
Scoring Ligand Similarity in Structure-Based Virtual Screening M.I. Zavodszky, A. Rohatgi, J. Van Voorst, H. Yan, L.A. Kuhn, submitted.
Synthetic curcuminoids modulate the arachidonic acid metabolism of human P-12-LOX and reduce sprout formation of human endothelial cells. J. Jankun, A.M. Aleem, S. Malgorzewicz, M. Szkudlarek, M.I. Zavodszky, D.L. DeWitt, M. Feig, S.H. Selman, E. Skrzypczak-Jankun. Molecular Cancer Therapeutics, 5(5):1371-82, 2006.
Structural Basis for the Enantiospecificities of R- and S-Specific Phenoxypropionate/Alpha-Ketoglutarate Dioxygenases. T.A. Muller, M.I. Zavodszky, M. Feig, L.A. Kuhn, and R.P. Hausinger. Protein Science, 6:1356-68, 2006.
Plasminogen activator inhibitor-1 is locked in active conformation and polymerizes upon binding ligands neutralizing its activity. J. Jankun, Z. Specht, M. Szkudlarek, R. Greenfield, B. Gaikwad, L. Trifonov, J. Vaugeois, A. A. Mukhtar, V. Basrur, S.H. Selman, M.I. Zavodszky , E. Skrzypczak-Jankun. International Journal of Molecular Medicine, 17(3):437-47, 2006.
Effect of crystal freezing and small molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution. E. Skrzypczak-Jankun, O.Y. Borbulevych, M.I. Zavodszky, M.R. Baranski, K. Padmanabhan, V. Petricek, J. Jankun Acta Cryst D62:766-775, 2006
An Efficient Empirical Scoring Function to Improve Docking Accuracy and Enrichment in Ligand Screening. L. He, M.I. Zavodszky, and L.A. Kuhn. Manuscript in preparation
Side-Chain Flexibility in Protein-Ligand Binding: The Minimal Rotation Hypothesis. M.I. Zavodszky and L.A. Kuhn Protein Science, 14:1104-1114, 2005.
Constraint Theory Applied to Proteins. M. Chubynsky, A.R. Day, B.M.Hespenheide, D.J. Jacobs, M. Lei, S. Menor, A.J. Rader, M.F. Thorpe, W. Whiteley, and M.I. Zavodszky. Proceedings of the workshop "Nano-Scale Materials: From Science to Technology", Puri, India, 2004, Nova Publishers.
Flexibility in Biomolecules. M.F. Thorpe, M. Chubynsky, B.M. Hespenheide, S. Menor, A.R. Day, D.J. Jacobs, L.A. Kuhn, M.I. Zavodszky, M. Lei, A.J. Rader, W. Whiteley. Current Topics in Physics, Edited by R.A.. Barrio and K.K. Kaski, Imperial College Press (London, 2005), Chapter 6, pages 97-112.
Modeling Correlated Main-Chain Motions in Proteins for Flexible Molecular Recognition. M.I. Zavodszky, M. Lei, M.F. Thorpe, A.R. Day, and L.A. Kuhn. Proteins, 57(2):243-61, 2004.
Sampling Protein Conformations and Pathways. M. Lei, M.I. Zavodszky, L.A. Kuhn, M.F. Thorpe. Journal of Computational Chemistry, 25(9):1133-1148, 2004.
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. M.I. Zavodszky, P.C. Sanschagrin, R.S. Korde, and L.A. Kuhn. Journal of Computer Aided Molecular Design, 16(12):883-902, 2002.
One Site Fits Both: A Model for the Ternary Complex of Folate +NADPH in R67 Dihydrofolate Reductase, a D2 Symmetric Enzyme. E.E. Howell, U. Shukla, S.N. Hicks, R.D. Smiley, L.A. Kuhn, and M.I. Zavodszky. Journal of Computer Aided Molecular Design, 15(11):10351052, 2001.
Disulfide Bond Effects on Protein Stability: Designed Variants of Cucurbita Maxima Trypsin Inhibitor-V. M.I. Zavodszky, C.W. Chen, J.K. Huang, M. Zolkiewski, L. Wen, and R. Krishnamoorthi. Protein Science 10(1):149-160, 2001.
Invited Presentations
Structure-Based Computational Screening in Drug Discovery.
Soft Matter Seminar Series, Dept. Physics and Astronomy, Arizona State University. November 17, 2004, Tempe, AZ
Docking Into Flexible Targets: A Two-Step Approach.
Modeling Protein Flexibility and Motions Worshop. July 17-22, 2004, Banff, Canada
Modeling Protein Flexibility in Docking
5th Canadian Conference of Computational Chemistry. July 26-30, 2003, Toronto, Canada
Modeling Induced Fit in Screening for New Ligands
E.I. DuPont, Crop Protection Products, SteinHaskell Research Center. June 28, 2002, Newark, DE
Conference Contributions - Oral Presentations
Flexibility in Molecular Recognition .
Midwest Computational Structural Biology Workshop. April 30 - May 1, 2005, Brook Lodge, Augusta, MI
Modeling Flexibility in Molecular Recognition .
36th Midwest Theoretical Chemistry Conference. June 17-19, 2004, East Lansing, MI
Conference Contributions - Posters
Flexibility at protein-protein and protein-ligand interfaces
M.I. Zavodszky and L.A. Kuhn
Modeling of protein interactions in genomes. June 26-28, 2005, Lawrence, KS
Rigidity Optimized Conformational Kinetics to Explore Protein Conformational Space
M. Lei, M. F. Thorpe, L. A. Kuhn and M. I. Zavodszky
225th American Chemical Society National Meeting.
March 2003, New Orleans
New ligands identified for thrombin by virtual screening
M.I. Zavodszky, M. Zolkiewski, L.A. Kuhn
Spring Symposium of the Center for Biological Modeling, MSU.
June 10, 2002, East Lansing, MI
Modeling protein main chain flexibility in ligand docking and screening: How much flexing is tolerated?
M.I. Zavodszky, M. Lei, M.F. Thorpe, L.A. Kuhn
The 16th Symposium of the Protein Society.
August 17-21, 2002, San Diego, CA
Rigidity Optimized Constrained Kinetics to Explore Protein Conformational Space
M. Lei, M. I. Zavodszky, A. Roy Day, L. A. Kuhn and M. F. Thorpe
The 16th Symposium of the Protein Society.
August 17-21, 2002, San Diego, CA
Realistic Modeling of Polar Interactions in Ligand Screening
M.I. Zavodszky, P. Sanschagrin, L.A. Kuhn
What makes a drug attractive for its receptor? ADMET, Affinity & Selectivity.
March 19-22, 2001, Schloss Rauischholzhausen, Marburg, Germany
Modeling of hydrophobic interactions in computational ligand screening: A template-matching approach
P.C. Sanschagrin, M.I. Zavodszky, L.A. Kuhn
What makes a drug attractive for its receptor? ADMET, Affinity & Selectivity. March 19-22, 2001, Schloss Rauischholzhausen, Marburg, Germany
Induced fit in Database Screening
M.I. Zavodszky, P. Sanschagrin, L.A. Kuhn
Protein Flexibility and Folding Workshop. August 2000, Traverse City
Template-based computational screening for ligands including side-chain flexibility and interfacial solvent
P.C. Sanschagrin, M.I. Zavodszky, L.A. Kuhn
Intelligent Systems for Molecular Biology. August 2000, San Diego, CA
Theses
Modeling Flexibility in Protein-Ligand Recognition
PhD thesis, Michigan State University, East Lansing, MI, 2003 Disulfide Bond Effects on Protein Stability: Designed Variants of Cucurbita Maxima Trypsin Inhibitor-V
MS thesis, Kansas State University, Manhattan, KS, 1999
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