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Document Acknowledgments Page 556 We thank J. Apostolakis and Professor A. Plückthun for helpful discussions. The calculations were performed on an SGI Indigo2 and an eight-processor SGI Challenge (R4400 processors). The CHARMM program within the version 4.0 of the QUANTA software package (Biosym-MSI Inc) was used for some of the minimization performed in this work. The CCLD program is available from A. Caflisch. This work was supported by the Swiss National Science Foundation (Schweizerischer Nationalfonds grant nr. 3100-043423.95) and by Novartis Pharma Inc. References 1. Gubernator K, Broger C, Bur D, Doran DM, Gerber PR, Müller K, Schaumann TM. Structure-based ligand design. In: Hermann EC, Frankle R, eds. Computer-Aided Drug Design in Industrial Research 1995:61–77. 2. Müller K. Paradigms of rational molecular design. In: Schwartz TW, Hjorth SA, Kastrup JS, eds. Structure and Function of 7TM Receptors, in press. 3. Gerber PR, Gubernator K, Müller K. Generic shapes for the conformational analysis of macrocyclic structures. Helv Chim Acta 1988; 71:1429–1441. 4. Böhm HJ. The computer program LUDI: a new method for de novo design of enzyme inhibitors. J Comput-Aided Mol Design 1992; 6:61–78. 5. Böhm HJ. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput-Aided Mol Design 1992; 6:593–606. 6. Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput-Aided Mol Design 1994; 8:243–256. 7. Böhm HJ. On the use of LUDI to search the fine chemicals directory for ligands of proteins of known three-dimensional structure. J Comput-Aided Mol Design 1994; 8:623–632. 8. Böhm HJ. Site-directed structure generation by fragment-joining. Perspectives in Drug Discovery and Design 1995; 3:21–33. 9. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985; 28:849–857. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_556.html (1 of 3) [4/9/2004 12:53:38 AM]
Document 10. Bobbyer DNA, Goodford PJ, McWhinnie PM, Wade RC. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem 1989; 32:1083–1094. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_556.html (2 of 3) [4/9/2004 12:53:38 AM] 11. Wade RC, Clark KJ, Goodford PJ. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J Med Chem 1993; 36:140–147.
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Structure-based Drug Design 14 Stru
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Document Cyclotheonamide A (CtA), 2
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document fragment-based programs, 5
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Document [Human immunodeficiency vi
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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