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0012972944
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The use of molecular modelling to discover and design new molecules
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of special interest. Longman Publishers Ltd Singapore This is the first book to appear which provides an extensive description of modern methods of molecular modelling. Chapter 10 provides a good introduction to the methods of drug design
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Leach AR. The use of molecular modelling to discover and design new molecules. of special interest Molecular Modelling Principles and Applications. 1996;543-585 Longman Publishers Ltd, Singapore, This is the first book to appear which provides an extensive description of modern methods of molecular modelling. Chapter 10 provides a good introduction to the methods of drug design.
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Molecular Modelling Principles and Applications
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Leach, A.R.1
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Discovery of HIV-1 integrase inhibitors by pharmacophore searching
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Hong H, Neamati N, Wang S, Nicklaus MC, Mazumder A, Zhao H, Burke TR Jr, Pommier Y, Milne GWA. Discovery of HIV-1 integrase inhibitors by pharmacophore searching. J Med Chem. 40:1997;930-936.
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Clinically effective HIV-1 protease inhibitors
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of special interest. A useful overview of the process of drug discovery for a set of four HIV-1 protease inhibitors which are now entering the market. The review outlines the approaches taken by the research groups in discovering the clinical compounds, the problems encountered during this process and their subsequent solutions.
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Vacca JP, Condra JH. Clinically effective HIV-1 protease inhibitors. of special interest Drug Discov Today. 2:1997;261-272 A useful overview of the process of drug discovery for a set of four HIV-1 protease inhibitors which are now entering the market. The review outlines the approaches taken by the research groups in discovering the clinical compounds, the problems encountered during this process and their subsequent solutions.
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Thaisrivongs S, Romero DL, Tommasi RA, Janakiraman MN, Strohbach JW, Turner SR, Biles C, Morge RR, Johnson PD, Aristoff PA, et al. Structure-based design of HIV protease inhibitors: 5,6-dihydro-4-hydroxy-2-pyrones as effective, nonpeptidic inhibitors. J Med Chem. 39:1996;4630-4642.
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Thaisrivongs, S.1
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Structure-based design of nonpeptidic HIV protease inhibitors: The sulfonamide-substituted cyclooctylpyranones
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Skulnick HI, Johnson PD, Aristoff PA, Morris JK, Lovasz KD, Howe WJ, Watenpaugh KD, Janakiraman MN, Anderson DJ, Reischer RJ, et al. Structure-based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyranones. J Med Chem. 40:1997;1149-1164.
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Melnick, M.1
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Dawson, H.7
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Protein structure-based design, synthesis, and biological evaluation of 5-thia-2, 6-diamino-4(3H)-oxopyrimidines: Potent inhibitors of glycinamide ribonucleotide transformylase with potent cell growth inhibition
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Varney MD, Palmer CL, Romines WH III, Boritzki T, Margosiak SA, Almassy R, Janson CA, Bartlett C, Howland EJ, Ferre R. Protein structure-based design, synthesis, and biological evaluation of 5-thia-2, 6-diamino-4(3H)-oxopyrimidines: potent inhibitors of glycinamide ribonucleotide transformylase with potent cell growth inhibition. J Med Chem. 40:1997;2502-2524.
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Varney, M.D.1
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0030893008
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Structure-based design of a potent, selective, and irreversible inhibitor of the catalytic domain of the erbB receptor subfamily of protein tyrosine kinases
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Singh J, Dobrusin EM, Fry DW, Haske T, Whitty A, McNamara DJ. Structure-based design of a potent, selective, and irreversible inhibitor of the catalytic domain of the erbB receptor subfamily of protein tyrosine kinases. J Med Chem. 40:1997;1130-1135.
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Structure-based design of a potent transition state analogue for TEM-1 β-lactamase
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Strynadka NCJ, Martin R, Jensen SE, Gold M, Jones JB. Structure-based design of a potent transition state analogue for TEM-1 β-lactamase. Nat Struct Biol. 3:1996;688-695.
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Strynadka, N.C.J.1
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Design of highly potent noncovalent thrombin inhibitors that utilize a novel lipophilic binding pocket in the thrombin active site
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Tucker TJ, Lumma WC, Mulichak AM, Chen Z, Naylor-Olsen AM, Lewis SD, Lucas R, Freidinger RM, Kuo LC. Design of highly potent noncovalent thrombin inhibitors that utilize a novel lipophilic binding pocket in the thrombin active site. J Med Chem. 40:1997;830-832.
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Tucker, T.J.1
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Structure-based design of substituted diphenyl sulfones and sulfoxides as lipophilic inhibitors of thymidylate synthase
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Jones TR, Webber SE, Varney MD, Reddy MR, Lewis KK, Kathardekar V, Mazdiyasni H, Deal J, Nguyen D, Welsh KM, et al. Structure-based design of substituted diphenyl sulfones and sulfoxides as lipophilic inhibitors of thymidylate synthase. J Med Chem. 40:1997;677-683.
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Jones, T.R.1
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0027287506
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Rational design of potent sialidase-based inhibitors of influenza virus replication
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Von Itzstein M, Wu WY, Kok GB, Pegg MS, Dyason JC, Jin B, Phan TV, Smythe ML, White HF, Oliver SW, et al. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature. 363:1993;418-423.
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0030272169
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Design and synthesis of carbohydrate-based inhibitors of protein-carbohydrate interactions
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of special interest. This paper reviews aspects of sialic acid biology and chemistry with relation to their biological functions and details work towards the development of potential therapeutic agents. Includes an overview of the work on design of sialidase-based inhibitors, which are now in final trials as anti-flu drugs - one of the most straightforward examples of structure-based design.
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Von Itzstein M, Colman P. Design and synthesis of carbohydrate-based inhibitors of protein-carbohydrate interactions. of special interest Curr Opin Struct Biol. 6:1996;703-709 This paper reviews aspects of sialic acid biology and chemistry with relation to their biological functions and details work towards the development of potential therapeutic agents. Includes an overview of the work on design of sialidase-based inhibitors, which are now in final trials as anti-flu drugs - one of the most straightforward examples of structure-based design.
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Curr Opin Struct Biol
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Von Itzstein, M.1
Colman, P.2
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Sialic acids and sialic acid-recognising proteins: Drug discovery targets and potential glycopharmaceuticals
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Von Itzstein M, Thomson RJ. Sialic acids and sialic acid-recognising proteins: drug discovery targets and potential glycopharmaceuticals. Cur Med Chem. 4:1997;185-210.
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Cur Med Chem
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Von Itzstein, M.1
Thomson, R.J.2
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0031189711
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Molecular recognition of protein - Ligand complexes: Applications to drug design
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of outstanding interest. A colossal review covering the 20 years of literature ending September 1996. The review covers the literature of the structures of complexes between small molecule ligands and several enzymes which are relevant as drug targets. A goal of the review is to enhance the qualitative understanding of protein - ligand complexes, providing analogies that could assist in structure-based design process.
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Babine RE, Bender SL. Molecular recognition of protein - ligand complexes: applications to drug design. of outstanding interest Chem Rev. 97:1997;1359-1472 A colossal review covering the 20 years of literature ending September 1996. The review covers the literature of the structures of complexes between small molecule ligands and several enzymes which are relevant as drug targets. A goal of the review is to enhance the qualitative understanding of protein - ligand complexes, providing analogies that could assist in structure-based design process.
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Chem Rev
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Babine, R.E.1
Bender, S.L.2
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Recognition of DNA by designed ligands and subnanomolar concentrations
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Trauger JW, Baird EE, Dervan PB. Recognition of DNA by designed ligands and subnanomolar concentrations. Nature. 382:1996;559-561.
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Nature
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Trauger, J.W.1
Baird, E.E.2
Dervan, P.B.3
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17
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0031045487
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Structure-based design of a new bisintercalating anthracycline antibiotic
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Chaires JB, Leng F, Przewloka T, Fokt I, Ling YH, Perez-Soler R, Priebe W. Structure-based design of a new bisintercalating anthracycline antibiotic. J Med Chem. 40:1997;261-266.
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J Med Chem
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Chaires, J.B.1
Leng, F.2
Przewloka, T.3
Fokt, I.4
Ling, Y.H.5
Perez-Soler, R.6
Priebe, W.7
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Current methods for site-directed structure generation
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Lewis RA, Leach AR. Current methods for site-directed structure generation. J Comput Aided Mol Des. 8:1994;467-475.
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Lewis, R.A.1
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Current computational tools for de novo ligand design
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Böhm HJ. Current computational tools for de novo ligand design. Curr Opin Biotechnol. 7:1996;433-436.
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Böhm, H.J.1
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0030204057
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Towards the automatic design of synthetically accessible protein ligands: Peptides, amides and peptidomimetics
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Böhm HJ. Towards the automatic design of synthetically accessible protein ligands: peptides, amides and peptidomimetics. J Comput Aided Mol Des. 10:1996;265-272.
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Böhm, H.J.1
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Structure-based design of parasitic protease inhibitors
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Li R, Chen X, Gong B, Selzer PM, Li Z, Davidson E, Kurzban G, Miller RE, Nuzum EO, McKerrow JH. Structure-based design of parasitic protease inhibitors. Bioorg Med Chem. 4:1996;1421-1427.
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Bioorg Med Chem
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Li, R.1
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Miller, R.E.8
Nuzum, E.O.9
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0030474049
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What can we learn from molecular recognition in protein - Ligand complexes for the design of new drugs?
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of special interest. Int Ed. An excellent and thoughtful analysis of the available structural information on protein - ligand complexes. It includes some detailed analyses of the physical chemistry of molecular recognition, identifying the potential contributions to interaction energy between protein and ligand.
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Böhm HJ, Klebe G. What can we learn from molecular recognition in protein - ligand complexes for the design of new drugs? of special interest Int Ed Angew Chem. 35:1996;2588-2614 An excellent and thoughtful analysis of the available structural information on protein - ligand complexes. It includes some detailed analyses of the physical chemistry of molecular recognition, identifying the potential contributions to interaction energy between protein and ligand.
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Angew Chem
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Böhm, H.J.1
Klebe, G.2
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Computational methods to predict binding free energy in ligand-receptor complexes
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Ajay Murcko MA. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem. 38:1995;4953-4967.
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Ajay Murcko, M.A.1
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VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
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Head RD, Smythe ML, Oprea TI, Waller CL, Green SM, Marshall GR. VALIDATE: a new method for the receptor-based prediction of binding affinities of novel ligands. J Am Chem Soc. 118:1996;3959-3969.
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Head, R.D.1
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Oprea, T.I.3
Waller, C.L.4
Green, S.M.5
Marshall, G.R.6
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26
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13344282748
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An approach to rapid estimation of relative binding affinities of enzyme inhibitors: Applications to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease
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Viswanadhan VN, Reddy MR, Wlodawer A, Varney MD, Weinstein JN. An approach to rapid estimation of relative binding affinities of enzyme inhibitors: applications to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease. J Med Chem. 39:1996;705-712.
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Reddy, M.R.2
Wlodawer, A.3
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Weinstein, J.N.5
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The development of a simple empirical scoring function to estimate the binding constant for a protein - Ligand complex of known three-dimensional structure
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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 Des. 8:1994;243-256.
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Böhm, H.J.1
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18744427313
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Database of three-dimensional structures of HIV proteinases
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of special interest. Describes a publicly accessible resource, collecting together structures of HIV-protease - inhibitor complexes. The URL associated with this database also includes references to other World Wide Web sites where analyses and databases of protein - ligand interactions, and the methods used to analyse them, are available.
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Vondrasek J, Van Buskirk CP, Wlodawer A. Database of three-dimensional structures of HIV proteinases. of special interest Nat Struct Biol. 4:1997;8 Describes a publicly accessible resource, collecting together structures of HIV-protease - inhibitor complexes. The URL associated with this database also includes references to other World Wide Web sites where analyses and databases of protein - ligand interactions, and the methods used to analyse them, are available.
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Nat Struct Biol
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Vondrasek, J.1
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Lam KS, Lebl M, Krchnák V. The "one-bead-one-compound" combinatorial library method. Chem Rev. 97:1997;411-448.
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Chem Rev
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Lebl, M.2
Krchnák, V.3
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31
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0030062879
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Protein structure-based combinatorial chemistry: Discovery of non-peptide binding elements to Src SH3 domain
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of special interest. One of the first examples of the use of structural information to guide the design of biased combinatorial libraries in the search for high-affinity inhibitors. The paper demonstrates that protein structure-based combinatorial chemistry is an effective method for identifying novel ligands containing non-peptide binding elements, in this particular case directed to the specificity packet of SH3 domains.
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Combs AP, Kapoor TM, Feng S, Chen JK, Daudé-Snow LF, Schreiber SL. Protein structure-based combinatorial chemistry: discovery of non-peptide binding elements to Src SH3 domain. of special interest J Am Chem Soc. 118:1996;287-288 One of the first examples of the use of structural information to guide the design of biased combinatorial libraries in the search for high-affinity inhibitors. The paper demonstrates that protein structure-based combinatorial chemistry is an effective method for identifying novel ligands containing non-peptide binding elements, in this particular case directed to the specificity packet of SH3 domains.
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J Am Chem Soc
, vol.118
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Combs, A.P.1
Kapoor, T.M.2
Feng, S.3
Chen, J.K.4
Daudé-Snow, L.F.5
Schreiber, S.L.6
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Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis
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Feng S, Kapoor TM, Shirai F, Combs AP, Schreiber SL. Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis. Chem Biol. 3:1996;661-670.
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Feng, S.1
Kapoor, T.M.2
Shirai, F.3
Combs, A.P.4
Schreiber, S.L.5
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Serendipity meets precision: The integration of structure-based drug design and combinatorial chemistry for efficient drug discovery
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Salemme FR, Spurlino J, Bone R. Serendipity meets precision: the integration of structure-based drug design and combinatorial chemistry for efficient drug discovery. Structure. 5:1997;319-324.
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Salemme, F.R.1
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Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm
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Weber L, Wallbaum S, Broger C, Gubernator K. Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm. Int Ed Angew Chem. 34:1995;2280-2282.
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Designing combinatorial library mixtures using a genetic algorithm
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Brown RD, Martin YC. Designing combinatorial library mixtures using a genetic algorithm. J Med Chem. 40:1997;2304-2313.
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J Med Chem
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Brown, R.D.1
Martin, Y.C.2
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0030916603
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Recent solution structures of RNA and its complexes with drugs, peptides and proteins
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of special interest. A useful overview of the available structural information on RNA molecules, which are becoming established as potential therapeutic targets.
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Ramos A, Gubser CC, Varani G. Recent solution structures of RNA and its complexes with drugs, peptides and proteins. of special interest Curr Opin Struct Biol. 7:1997;317-323 A useful overview of the available structural information on RNA molecules, which are becoming established as potential therapeutic targets.
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Curr Opin Struct Biol
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, pp. 317-323
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Ramos, A.1
Gubser, C.C.2
Varani, G.3
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An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication
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Hamy F, Felder ER, Heizmann G, Lazdins J, Aboul-Ela F, Varani G, Karn J, Klimkait T. An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. Proc Natl Acad Sci USA. 94:1997;3548-3553.
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Hamy, F.1
Felder, E.R.2
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Lazdins, J.4
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Varani, G.6
Karn, J.7
Klimkait, T.8
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39
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0029836953
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Discovering high-affinity ligands for proteins: SAR by NMR
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of outstanding interest. The development of this new NMR-based technique is the most important development in structure-based drug design of the past two years. This paper describes the techniques employed, and their application to the discovery of novel inhibitors for FKBP.
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Shuker SB, Hajduk PJ, Meadows RP, Fesik SW. Discovering high-affinity ligands for proteins: SAR by NMR. of outstanding interest Science. 274:1996;1531-1534 The development of this new NMR-based technique is the most important development in structure-based drug design of the past two years. This paper describes the techniques employed, and their application to the discovery of novel inhibitors for FKBP.
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Science
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Shuker, S.B.1
Hajduk, P.J.2
Meadows, R.P.3
Fesik, S.W.4
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40
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16944365890
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Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR
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of outstanding interest. This paper provides an excellent example of the further application of structure-activity relationships by NMR technique to develop inhibitors for an enzyme, in this case stromelysin, a matrix metaloproteinase which is a potential target in the in the treatment of arthritis. The co-published paper, Olejiniczak et al. 1997 [41], provides further thermodynamic analysis of how the technique works.
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Hajduk PJ, Sheppard G, Nettesheim DG, Olejniczak ET, Shuker SB, Meadows RP, Steinman DH, Carrera GM Jr, Marcotte PA, Severin J, et al. Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. of outstanding interest J Am Chem Soc. 119:1997;5818-5827 This paper provides an excellent example of the further application of structure-activity relationships by NMR technique to develop inhibitors for an enzyme, in this case stromelysin, a matrix metaloproteinase which is a potential target in the in the treatment of arthritis. The co-published paper, Olejiniczak et al. 1997 [41], provides further thermodynamic analysis of how the technique works.
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J Am Chem Soc
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Hajduk, P.J.1
Sheppard, G.2
Nettesheim, D.G.3
Olejniczak, E.T.4
Shuker, S.B.5
Meadows, R.P.6
Steinman, D.H.7
Carrera G.M., Jr.8
Marcotte, P.A.9
Severin, J.10
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41
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0030829408
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Stromelysin inhibitors designed from weakly bound fragments: Effects of linking and cooperativity
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An experimental approach to mapping the binding surfaces of crystalline proteins
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Virtual combinatorial libraries: Dynamic generation of molecular and supramolecular diversity by self-assembly
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of outstanding interest. A fascinating new idea, where potential inhibitors self-assemble on the surface of a protein based on the relative affinity of molecular fragments for the protein binding surfaces.
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