MSU SLIDE ('Screening for Ligands by Induced-fit Docking, Efficiently') represents a general approach to organic and peptidyl database screening. It can handle large binding-site templates and uses multi-stage indexing to identify feasible subsets of template points for ligand docking. An optimization approach based on mean-field theory is applied to model induced-fit complementarity, balancing flexibility between the ligand and the protein side chains. SLIDE can screen 100,000 compounds within a few days and returns a ranked list of sterically feasible ligand candidates, ranked by complementarity to the protein's binding site.
SLIDE is available for licensing to academic and commercial researchers. Please see the section on License Agreements below for more information.
Publications related to SLIDE include the following:
- M. I. Zavodszky, A. Rohatgi, J. R. Van Voorst, H. Yan, and L. A. Kuhn (2009) "Scoring Ligand Similarity in Structure-Based Virtual Screening" (pdf), Journal of Molecular Recognition
- L. A. Kuhn (2008) "Strength in Flexibility: Modeling Side-chain Conformational Change in Docking and Screening" (pdf), Structure-Based Drug Discovery (R. M. Stroud and J. Finer-Moore, Eds.), Royal Society of Chemistry, London
- P. Cozzini, G. E. Kellogg, F. Spyrakis, D. J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L. A. Kuhn, G. M. Morris, M. Orozco, T. A. Pertinhez, M. Rizzi, and C. A. Sotriffer (2008) "Target Flexibility: An Emerging Consideration in Drug Discovery and Design" (pdf), J. Med. Chem. 51, 6237-6255.
- M. Chubynsky, B. Hespenheide, D. J. Jacobs, L. A. Kuhn, M. Lei, S. Menor, A. J. Rader, M. F. Thorpe,W. Whiteley, and M. I. Zavodszky (2006) "Constraint Theory Applied to Proteins", in Nano-Scale Materials: From Science to Technology", (S. N. Sahu, R. K. Choudhury, and P. Jena, eds.), Nova Publishers, Hauppauge New York, pp. 77-88.
- T. A. Muller, M. I. Zavodszky, M. Feig, L. A. Kuhn, and R. P. Hausinger (2006) "Structural Basis for the Enantiomeric Specificities of R- and S-specific Phenoxypropionate/Alpha-ketoglutarate Dioxygenases" (pdf), Protein Science 15, 1356-1368.
- S. C. K. Sukuru, T. Crepin, Y. Milev, L. C. Marsh, J. B. Hill, R. J. Anderson, J. C. Morris, A. Rohatgi, G. O'Mahony, M. Grotli, F. Danel, Y. Milev, M. G. P. Page, M. Hartlein, S. Cusack, M. A. Kron, and L. A. Kuhn (2006) "Discovering New Classes of Brugia malayi Asparaginyl tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change" (pdf), J. Comp.-Aided Molec. Design 20, 159-178.
- M.I. Zavodszky, L.A. Kuhn (2005) "Side-Chain Flexibility in Protein-Ligand Binding: The Minimal Rotation Hypothesis" (pdf), Protein Science, 14, 1104 - 1114.
- M. I. Zavodszky, M. Lei, A. R. Day, M. F. Thorpe, and L. A. Kuhn (2004) "Modeling Correlated Main-chain Motions in Proteins for Flexible Molecular Recognition" (pdf), Proteins: Struct. Funct. Bioinf., 57(2):243-261.
- H. Gohlke, L. A. Kuhn, and D. A. Case (2004) "Change in Protein Flexibility Upon Complex Formation: Analysis of Ras-Raf Using Molecular Dynamics and Molecular Approach" (pdf), Proteins: Struct. Funct. Bioinf., 56:322-337.
- M. I. Zavodszky, P. C. Sanschagrin, R. S. Korde, and L. A. Kuhn (2002) "Distilling the Essential Features of a Protein Surface for Improving Protein-Ligand Docking, Scoring, and Virtual Screening" (pdf), J. Comp.-Aided Molecular Design, 16, 883-902.
- E. E. Howell, U. Shukla, S. N. Hicks, R. D. Smiley, L. A. Kuhn, and M. I. Zavodszky (2001) "One Site Fits Both: A Model for the Ternary Complex of Folate + NADPH in R67 Dihydrofolate Reductase, a D2 Symmetric Enzyme" (pdf), J. Computer-Aided Molec. Design, 15, 1035-1052.
- V. Schnecke and L. A. Kuhn (2000) "Virtual Screening with Solvation and Ligand-Induced Complementarity" (pdf), Perspectives in Drug Design and Discovery, 20, 171-190.
- V. Schnecke and L. A. Kuhn (1999) "Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity" (pdf), Proceedings of the Seventh International Conference in Intelligent Systems for Molecular Biology, AAAI Press, pp. 242-251.
- V. Schnecke and L. A. Kuhn (1999) "Flexibly Screening for Molecules Interacting with Proteins" (pdf), in Rigidity Theory and Applications (M. F. Thorpe and P. M. Duxbury, eds.), Plenum Publishing, New York, pp. 385-400.
- V. Schnecke, C. A. Swanson, E. D. Getzoff, J. A. Tainer, and L. A. Kuhn (1998) "Screening a Peptidyl Database for Potential Ligands to Proteins with Side-chain Flexibility" (pdf), Proteins: Structure, Function, and Genetics, 33, 74-87.
SLIDE user manuals, quick guides, and flyers:
A detailed SLIDE Tutorial is now available for download, which covers v. 3.3.5 as well as the newly released version 3.4.
Please see the steps in the SLIDE Quick Guide for a quick overview and examples of running SLIDE. Email [email protected], with any further questions.
For installation instruction, please see docu/installation_instructions.txt.
SLIDE is now available for licensing to academic and commercial researchers. To arrange a license or for scientific inquiries, please contact:
Leslie Kuhn
502C Biochemistry Building
MSU, East Lansing, MI 48824
Telephone: (517) 353-8745
E-mail: [email protected]
Version 3.4 of the SLIDE Release Notes are now available for download below. For those users of previous versions of SLIDE who wish to upgrade, please email the authors at [email protected].
Scientific Support and Licensing Information
Dr. Leslie Kuhn
Protein Structural Analysis and Design Lab
502C Biochemistry
Michigan State University
East Lansing, MI 48823
Tel: 517-355-8745
Fax: 517-353-9334
Email: [email protected]