메뉴 건너뛰기




Volumn 326, Issue 2, 2003, Pages 621-636

Utilising structural knowledge in drug design strategies: Applications using relibase

Author keywords

3D database; Data mining; Protein ligand interaction; Structure based drug design

Indexed keywords

2 [4 [(1 ACETIMIDOYL 3 PYRROLIDINYL)OXY]PHENYL] 3 (7 AMIDINO 2 NAPHTHYL)PROPIONIC ACID; ADENYLATE KINASE; ALDEHYDE REDUCTASE; ALDOSE REDUCTASE INHIBITOR; ANTICOAGULANT AGENT; BLOOD CLOTTING FACTOR 10A; BLOOD CLOTTING FACTOR 10A INHIBITOR; CARBONATE DEHYDRATASE; CARBONATE DEHYDRATASE INHIBITOR; IMMUNOTOXIN; LIGAND; PLASMINOGEN ACTIVATOR; PLASMINOGEN ACTIVATOR INHIBITOR; RICIN; THROMBIN; THROMBIN INHIBITOR; TRYPSIN; TRYPTASE; TRYPTASE INHIBITOR; WATER;

EID: 0037436333     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01409-2     Document Type: Article
Times cited : (99)

References (57)
  • 4
    • 0031866670 scopus 로고    scopus 로고
    • ACHEdb: The database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server
    • Cousin X., Hotelier T., Giles K., Toutant J.P., Chatonnet A. aCHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server. Nucl. Acids Res. 26:1998;226-228.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 226-228
    • Cousin, X.1    Hotelier, T.2    Giles, K.3    Toutant, J.P.4    Chatonnet, A.5
  • 5
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • White S.H., Wimley W.C. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28:1999;319-365.
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 7
  • 9
    • 0030896326 scopus 로고    scopus 로고
    • Promise: A new database of information on prosthetic centres and metal ions in protein active sites
    • Degtyarenko K.N., North A.C., Findlay J.B. Promise: a new database of information on prosthetic centres and metal ions in protein active sites. Protein Eng. 10:1997;183-186.
    • (1997) Protein Eng. , vol.10 , pp. 183-186
    • Degtyarenko, K.N.1    North, A.C.2    Findlay, J.B.3
  • 10
    • 0035170508 scopus 로고    scopus 로고
    • Collecting and harvesting biological data: The GPCRDB and NucleaRDB information systems
    • Horn F., Vriend G., Cohen F.E. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucl. Acids Res. 29:2001;346-349.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 346-349
    • Horn, F.1    Vriend, G.2    Cohen, F.E.3
  • 12
    • 0035175679 scopus 로고    scopus 로고
    • PDBsum: Summaries and analyses of PDB structures
    • Laskowski R.A. PDBsum: summaries and analyses of PDB structures. Nucl. Acids Res. 29:2001;221-222.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 221-222
    • Laskowski, R.A.1
  • 16
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 17
    • 0031865006 scopus 로고    scopus 로고
    • Touring protein fold space with Dali/FSSP
    • Holm L., Sander C. Touring protein fold space with Dali/FSSP. Nucl. Acids Res. 26:1998;316-319.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 316-319
    • Holm, L.1    Sander, C.2
  • 18
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick K., Thornton J.M. PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23:1998;358-361.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 19
    • 0036169718 scopus 로고    scopus 로고
    • The Binding Database: Data management and interface design
    • Chen X., Lin Y., Liu M., Gilson M.K. The Binding Database: data management and interface design. Bioinformatics. 18:2002;130-139.
    • (2002) Bioinformatics , vol.18 , pp. 130-139
    • Chen, X.1    Lin, Y.2    Liu, M.3    Gilson, M.K.4
  • 21
    • 0031827457 scopus 로고    scopus 로고
    • 3DinSight: An integrated relational database and search tool for the structure, function and properties of biomolecules
    • An J., Nakama T., Kubota Y., Sarai A. 3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules. Bioinformatics. 14:1998;188-195.
    • (1998) Bioinformatics , vol.14 , pp. 188-195
    • An, J.1    Nakama, T.2    Kubota, Y.3    Sarai, A.4
  • 22
    • 85031379591 scopus 로고    scopus 로고
    • Design and development of relibase: A database for comprehensive analysis of protein-ligand interactions
    • Hendlich, M., Bergner, A., Günther, J. & Klebe, G. (2002). Design and development of relibase: a database for comprehensive analysis of protein-ligand interactions. J. Mol. Biol.
    • (2002) J. Mol. Biol.
    • Hendlich, M.1    Bergner, A.2    Günther, J.3    Klebe, G.4
  • 24
    • 0030466444 scopus 로고    scopus 로고
    • Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
    • Ladbury J.E. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem. Biol. 3:1996;973-980.
    • (1996) Chem. Biol. , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 25
    • 0033587105 scopus 로고    scopus 로고
    • The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: Heat-labile enterotoxin, a multivalent test case
    • Minke W.E., Diller D.J., Hol W.G., Verlinde C.L. The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case. J. Med. Chem. 42:1999;1778-1788.
    • (1999) J. Med. Chem. , vol.42 , pp. 1778-1788
    • Minke, W.E.1    Diller, D.J.2    Hol, W.G.3    Verlinde, C.L.4
  • 26
    • 0033915678 scopus 로고    scopus 로고
    • Recent developments in structure-based drug design
    • Klebe G. Recent developments in structure-based drug design. J. Mol. Med. 78:2000;269-281.
    • (2000) J. Mol. Med. , vol.78 , pp. 269-281
    • Klebe, G.1
  • 27
    • 0033674405 scopus 로고    scopus 로고
    • Virtual screening with solvation and ligand-induced complementarity
    • Schnecke V., Kuhn L.A. Virtual screening with solvation and ligand-induced complementarity. Persp. Drug Discov. Des. 20:1999;171-190.
    • (1999) Persp. Drug Discov. Des. , vol.20 , pp. 171-190
    • Schnecke, V.1    Kuhn, L.A.2
  • 28
    • 0034996721 scopus 로고    scopus 로고
    • Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking(1)
    • Anderson A.C., O'Neil R.H., Surti T.S., Stroud R.M. Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking(1). Chem. Biol. 8:2001;445-457.
    • (2001) Chem. Biol. , vol.8 , pp. 445-457
    • Anderson, A.C.1    O'Neil, R.H.2    Surti, T.S.3    Stroud, R.M.4
  • 29
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: Efficient molecular docking considering protein structure variations
    • Claussen H., Buning C., Rarey M., Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 308:2001;377-395.
    • (2001) J. Mol. Biol. , vol.308 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 32
    • 0032585544 scopus 로고    scopus 로고
    • Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: Implications for the inhibition of factor Xa, tPA, and urokinase
    • Renatus M., Bode W., Huber R., Sturzebecher J., Stubbs M.T. Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinase. J. Med. Chem. 41:1998;5445-5456.
    • (1998) J. Med. Chem. , vol.41 , pp. 5445-5456
    • Renatus, M.1    Bode, W.2    Huber, R.3    Sturzebecher, J.4    Stubbs, M.T.5
  • 33
    • 0035910596 scopus 로고    scopus 로고
    • Subnanomolar inhibitors from computer screening: A model study using human carbonic anhydrase II
    • Grüneberg S., Wendt B., Klebe G. Subnanomolar inhibitors from computer screening: a model study using human carbonic anhydrase II. Angew. Chem. Int. Ed. Engl. 40:2001;389-393.
    • (2001) Angew. Chem. Int. Ed. Engl. , vol.40 , pp. 389-393
    • Grüneberg, S.1    Wendt, B.2    Klebe, G.3
  • 34
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Müller C.W., Schlauderer G.J., Reinstein J., Schulz G.E. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure. 4:1996;147-156.
    • (1996) Structure , vol.4 , pp. 147-156
    • Müller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 35
    • 0032147007 scopus 로고    scopus 로고
    • Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
    • Sandak B., Wolfson H.J., Nussinov R. Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers. Proteins: Struct. Funct. Genet. 32:1998;159-174.
    • (1998) Proteins: Struct. Funct. Genet. , vol.32 , pp. 159-174
    • Sandak, B.1    Wolfson, H.J.2    Nussinov, R.3
  • 36
    • 0029450365 scopus 로고
    • Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
    • Poornima C.S., Dean P.M. Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J. Comput. Aided Mol. Des. 9:1995;500-512.
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 500-512
    • Poornima, C.S.1    Dean, P.M.2
  • 37
    • 0029134561 scopus 로고
    • The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: Synthesis, biological activity, and crystallographic analysis with cyclophilin A
    • Mikol V., Papageorgiou C., Borer X. The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A. J. Med. Chem. 38:1995;3361-3367.
    • (1995) J. Med. Chem. , vol.38 , pp. 3361-3367
    • Mikol, V.1    Papageorgiou, C.2    Borer, X.3
  • 38
    • 0028057975 scopus 로고
    • Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
    • Lam P.Y., Jadhav P.K., Eyermann C.J., Hodge C.N., Ru Y., Bacheler L.T., et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science. 263:1994;380-384.
    • (1994) Science , vol.263 , pp. 380-384
    • Lam, P.Y.1    Jadhav, P.K.2    Eyermann, C.J.3    Hodge, C.N.4    Ru, Y.5    Bacheler, L.T.6
  • 39
    • 0029989480 scopus 로고    scopus 로고
    • A possible involvement of solvent-induced interactions in drug design
    • Wang H., Ben-Naim A. A possible involvement of solvent-induced interactions in drug design. J. Med. Chem. 39:1996;1531-1539.
    • (1996) J. Med. Chem. , vol.39 , pp. 1531-1539
    • Wang, H.1    Ben-Naim, A.2
  • 40
  • 41
    • 0030471364 scopus 로고    scopus 로고
    • The role of water in sequence-independent ligand binding by an oligopeptide transporter protein
    • Tame J.R., Sleigh S.H., Wilkinson A.J., Ladbury J.E. The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nature Struct. Biol. 3:1996;998-1001.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 998-1001
    • Tame, J.R.1    Sleigh, S.H.2    Wilkinson, A.J.3    Ladbury, J.E.4
  • 42
    • 0032806924 scopus 로고    scopus 로고
    • Relating structure to thermodynamics: The crystal structures and binding affinity of eight OppA-peptide complexes
    • Davies T.G., Hubbard R.E., Tame J.R. Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci. 8:1999;1432-1444.
    • (1999) Protein Sci. , vol.8 , pp. 1432-1444
    • Davies, T.G.1    Hubbard, R.E.2    Tame, J.R.3
  • 43
    • 0032961895 scopus 로고    scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey M., Kramer B., Lengauer T. The particle concept: placing discrete water molecules during protein-ligand docking predictions. Proteins: Struct. Funct. Genet. 34:1999;17-28.
    • (1999) Proteins: Struct. Funct. Genet. , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 44
    • 0028824422 scopus 로고
    • Crystal structures of factor Xa specific inhibitors in complex with trypsin: Structural grounds for inhibition of factor Xa and selectivity against thrombin
    • Stubbs M.T., Huber R., Bode W. Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin. FEBS Letters. 375:1995;103-107.
    • (1995) FEBS Letters , vol.375 , pp. 103-107
    • Stubbs, M.T.1    Huber, R.2    Bode, W.3
  • 46
    • 0027027467 scopus 로고
    • LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
    • Böhm H.J. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput. Aided Mol. Des. 6:1992;593-606.
    • (1992) J. Comput. Aided Mol. Des. , vol.6 , pp. 593-606
    • Böhm, H.J.1
  • 48
    • 0033530862 scopus 로고    scopus 로고
    • Blockers of human T cell Kv1.3 potassium channels using de novo ligand design and solid-phase parallel combinatorial chemistry
    • Lew A., Chamberlin A.R. Blockers of human T cell Kv1.3 potassium channels using de novo ligand design and solid-phase parallel combinatorial chemistry. Bioorg. Med. Chem. Letters. 9:1999;3267-3272.
    • (1999) Bioorg. Med. Chem. Letters , vol.9 , pp. 3267-3272
    • Lew, A.1    Chamberlin, A.R.2
  • 49
    • 0035936686 scopus 로고    scopus 로고
    • A new target for shigellosis: Rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase
    • Gradler U., Gerber H.D., Goodenough-Lashua D.M., Garcia G.A., Ficner R., Reuter K., et al. A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase. J. Mol. Biol. 306:2001;455-467.
    • (2001) J. Mol. Biol. , vol.306 , pp. 455-467
    • Gradler, U.1    Gerber, H.D.2    Goodenough-Lashua, D.M.3    Garcia, G.A.4    Ficner, R.5    Reuter, K.6
  • 50
    • 0033921051 scopus 로고    scopus 로고
    • Computer-aided design and activity prediction of leucine aminopeptidase inhibitors
    • Grembecka J., Sokalski W.A., Kafarski P. Computer-aided design and activity prediction of leucine aminopeptidase inhibitors. J. Comput. Aided Mol. Des. 14:2000;531-544.
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , pp. 531-544
    • Grembecka, J.1    Sokalski, W.A.2    Kafarski, P.3
  • 52
    • 0026587755 scopus 로고
    • Crystal structures of aconitase with isocitrate and nitroisocitrate bound
    • Lauble H., Kennedy M.C., Beinert H., Stout C.D. Crystal structures of aconitase with isocitrate and nitroisocitrate bound. Biochemistry. 31:1992;2735-2748.
    • (1992) Biochemistry , vol.31 , pp. 2735-2748
    • Lauble, H.1    Kennedy, M.C.2    Beinert, H.3    Stout, C.D.4
  • 54
    • 0035801603 scopus 로고    scopus 로고
    • From structure to function: A new approach to detect functional similarity among proteins independent from sequence and fold homology
    • Schmitt S., Hendlich M., Klebe G. From structure to function: a new approach to detect functional similarity among proteins independent from sequence and fold homology. Angew. Chem. Int Ed. Engl. 40:2001;3141-3144.
    • (2001) Angew. Chem. Int Ed. Engl. , vol.40 , pp. 3141-3144
    • Schmitt, S.1    Hendlich, M.2    Klebe, G.3
  • 55
    • 0001731266 scopus 로고    scopus 로고
    • Use of Relibase for retrieving complex 3D interaction patterns including crystallographic packing effects
    • Bergner A., Günther J., Hendlich M., Klebe G., Verdonk M.L. Use of Relibase for retrieving complex 3D interaction patterns including crystallographic packing effects. Biopol. (Nucl. Acid Sci.). 61:2002;99-110.
    • (2002) Biopol. (Nucl. Acid Sci.) , vol.61 , pp. 99-110
    • Bergner, A.1    Günther, J.2    Hendlich, M.3    Klebe, G.4    Verdonk, M.L.5
  • 57
    • 0034089394 scopus 로고    scopus 로고
    • A closer view of the conformation of the Lac repressor bound to operator
    • Bell C.E., Lewis M. A closer view of the conformation of the Lac repressor bound to operator. Nature Struct. Biol. 7:2000;209-214.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 209-214
    • Bell, C.E.1    Lewis, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.