메뉴 건너뛰기




Volumn 359, Issue 4, 2006, Pages 1023-1044

From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase

Author keywords

classification of protein binding pockets; cluster analysis of protein binding pockets; protein binding pockets; protein kinases; SARS protease

Indexed keywords

LIGAND; PROTEIN KINASE; PROTEINASE;

EID: 33744935012     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.024     Document Type: Article
Times cited : (84)

References (84)
  • 2
    • 0035782687 scopus 로고    scopus 로고
    • Review: what can structural classifications reveal about protein evolution?
    • Orengo C.A., Sillitoe I., Reeves G., and Pearl F.M. Review: what can structural classifications reveal about protein evolution?. J. Struct. Biol. 134 (2001) 145-165
    • (2001) J. Struct. Biol. , vol.134 , pp. 145-165
    • Orengo, C.A.1    Sillitoe, I.2    Reeves, G.3    Pearl, F.M.4
  • 3
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions
    • Nagano N., Orengo C.A., and Thornton J.M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321 (2002) 741-765
    • (2002) J. Mol. Biol. , vol.321 , pp. 741-765
    • Nagano, N.1    Orengo, C.A.2    Thornton, J.M.3
  • 4
    • 0037304408 scopus 로고    scopus 로고
    • Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins
    • Anantharaman V., Aravind L., and Koonin E.V. Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins. Curr. Opin. Chem. Biol. 7 (2003) 12-20
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 12-20
    • Anantharaman, V.1    Aravind, L.2    Koonin, E.V.3
  • 5
    • 1642540579 scopus 로고    scopus 로고
    • Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition
    • Weber A., Casini A., Heine A., Kuhn D., Supuran C.T., Scozzafava A., and Klebe G. Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition. J. Med. Chem. 47 (2004) 550-557
    • (2004) J. Med. Chem. , vol.47 , pp. 550-557
    • Weber, A.1    Casini, A.2    Heine, A.3    Kuhn, D.4    Supuran, C.T.5    Scozzafava, A.6    Klebe, G.7
  • 6
    • 0027967593 scopus 로고
    • A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
    • Artymiuk P.J., Poirrette A.R., Grindley H.M., Rice D.W., and Willett P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol. 243 (1994) 327-344
    • (1994) J. Mol. Biol. , vol.243 , pp. 327-344
    • Artymiuk, P.J.1    Poirrette, A.R.2    Grindley, H.M.3    Rice, D.W.4    Willett, P.5
  • 7
    • 0038128338 scopus 로고    scopus 로고
    • Searching for patterns of amino acids in 3D protein structures
    • Spriggs R.V., Artymiuk P.J., and Willett P. Searching for patterns of amino acids in 3D protein structures. J. Chem. Inf. Comput. Sci. 43 (2003) 412-421
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 412-421
    • Spriggs, R.V.1    Artymiuk, P.J.2    Willett, P.3
  • 8
    • 0030724039 scopus 로고    scopus 로고
    • TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
    • Wallace A.C., Borkakoti N., and Thornton J.M. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6 (1997) 2308-2323
    • (1997) Protein Sci. , vol.6 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 9
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt G.J. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285 (1999) 1887-1897
    • (1999) J. Mol. Biol. , vol.285 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 10
    • 0037375799 scopus 로고    scopus 로고
    • Efficient identification of side-chain patterns using a multidimensional index tree
    • Hamelryck T. Efficient identification of side-chain patterns using a multidimensional index tree. Proteins: Struct. Funct. Genet. 51 (2003) 96-108
    • (2003) Proteins: Struct. Funct. Genet. , vol.51 , pp. 96-108
    • Hamelryck, T.1
  • 11
    • 0027238108 scopus 로고
    • A computer vision based technique for 3-D sequence-independent structural comparison of proteins
    • Bachar O., Fischer D., Nussinov R., and Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 6 (1993) 279-288
    • (1993) Protein Eng. , vol.6 , pp. 279-288
    • Bachar, O.1    Fischer, D.2    Nussinov, R.3    Wolfson, H.4
  • 12
    • 0027519425 scopus 로고
    • Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications
    • Fischer D., Wolfson H., and Nussinov R. Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications. J. Biomol. Struct. Dynam. 11 (1993) 367-380
    • (1993) J. Biomol. Struct. Dynam. , vol.11 , pp. 367-380
    • Fischer, D.1    Wolfson, H.2    Nussinov, R.3
  • 13
    • 0027168214 scopus 로고
    • Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition
    • Fischer D., Norel R., Wolfson H., and Nussinov R. Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition. Proteins: Struct. Funct. Genet. 16 (1993) 278-292
    • (1993) Proteins: Struct. Funct. Genet. , vol.16 , pp. 278-292
    • Fischer, D.1    Norel, R.2    Wolfson, H.3    Nussinov, R.4
  • 14
    • 0028230909 scopus 로고
    • Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding
    • Fischer D., Wolfson H., Lin S.L., and Nussinov R. Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Sci. 3 (1994) 769-778
    • (1994) Protein Sci. , vol.3 , pp. 769-778
    • Fischer, D.1    Wolfson, H.2    Lin, S.L.3    Nussinov, R.4
  • 15
    • 0029025913 scopus 로고
    • A geometry-based suite of molecular docking processes
    • Fischer D., Lin S.L., Wolfson H.L., and Nussinov R. A geometry-based suite of molecular docking processes. J. Mol. Biol. 248 (1995) 459-477
    • (1995) J. Mol. Biol. , vol.248 , pp. 459-477
    • Fischer, D.1    Lin, S.L.2    Wolfson, H.L.3    Nussinov, R.4
  • 16
    • 0029564871 scopus 로고
    • A 3D sequence-independent representation of the protein data bank
    • Fischer D., Tsai C.J., Nussinov R., and Wolfson H. A 3D sequence-independent representation of the protein data bank. Protein Eng. 8 (1995) 981-997
    • (1995) Protein Eng. , vol.8 , pp. 981-997
    • Fischer, D.1    Tsai, C.J.2    Nussinov, R.3    Wolfson, H.4
  • 18
    • 33744899353 scopus 로고    scopus 로고
    • Molecular recognition via face center representation of a molecular surface
    • Lin S.L., and Nussinov R. Molecular recognition via face center representation of a molecular surface. J. Mol. Graph. 78-90 (1996) 95-97
    • (1996) J. Mol. Graph. , vol.78-90 , pp. 95-97
    • Lin, S.L.1    Nussinov, R.2
  • 19
    • 0028166881 scopus 로고
    • Shape complementarity at protein-protein interfaces
    • Norel R., Lin S.L., Wolfson H.J., and Nussinov R. Shape complementarity at protein-protein interfaces. Biopolymers 34 (1994) 933-940
    • (1994) Biopolymers , vol.34 , pp. 933-940
    • Norel, R.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 20
    • 0031776823 scopus 로고    scopus 로고
    • Molecular shape comparisons in searches for active sites and functional similarity
    • Rosen M., Lin S.L., Wolfson H., and Nussinov R. Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng. 11 (1998) 263-277
    • (1998) Protein Eng. , vol.11 , pp. 263-277
    • Rosen, M.1    Lin, S.L.2    Wolfson, H.3    Nussinov, R.4
  • 21
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg A., Nussinov R., and Wolfson H.J. Recognition of functional sites in protein structures. J. Mol. Biol. 339 (2004) 607-633
    • (2004) J. Mol. Biol. , vol.339 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 22
    • 0031697713 scopus 로고    scopus 로고
    • A geometric algorithm to find small but highly similar 3D substructures in proteins
    • Pennec X., and Ayache N. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14 (1998) 516-522
    • (1998) Bioinformatics , vol.14 , pp. 516-522
    • Pennec, X.1    Ayache, N.2
  • 23
    • 0032568859 scopus 로고    scopus 로고
    • Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution
    • Russell R.B. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J. Mol. Biol. 279 (1998) 1211-1227
    • (1998) J. Mol. Biol. , vol.279 , pp. 1211-1227
    • Russell, R.B.1
  • 24
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures
    • Stark A., and Russell R.B. Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures. Nucl. Acids Res. 31 (2003) 3341-3344
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 25
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita K., Furui J., and Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics 2 (2002) 9-22
    • (2002) J. Struct. Funct. Genomics , vol.2 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 26
    • 0041842509 scopus 로고    scopus 로고
    • Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    • Kinoshita K., and Nakamura H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci. 12 (2003) 1589-1595
    • (2003) Protein Sci. , vol.12 , pp. 1589-1595
    • Kinoshita, K.1    Nakamura, H.2
  • 28
    • 0033557381 scopus 로고    scopus 로고
    • Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm
    • Lehtonen J.V., Denessiouk K., May A.C., and Johnson M.S. Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm. Proteins: Struct. Funct. Genet. 34 (1999) 341-355
    • (1999) Proteins: Struct. Funct. Genet. , vol.34 , pp. 341-355
    • Lehtonen, J.V.1    Denessiouk, K.2    May, A.C.3    Johnson, M.S.4
  • 30
    • 0037459071 scopus 로고    scopus 로고
    • Functional sites in protein families uncovered via an objective and automated graph theoretic approach
    • Wangikar P.P., Tendulkar A.V., Ramya S., Mali D.N., and Sarawagi S. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J. Mol. Biol. 326 (2003) 955-978
    • (2003) J. Mol. Biol. , vol.326 , pp. 955-978
    • Wangikar, P.P.1    Tendulkar, A.V.2    Ramya, S.3    Mali, D.N.4    Sarawagi, S.5
  • 31
  • 32
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt S., Kuhn D., and Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 323 (2002) 387-406
    • (2002) J. Mol. Biol. , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 34
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: a quarter of a million crystal structures and rising
    • Allen F.H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallog. sect. B 58 (2002) 380-388
    • (2002) Acta Crystallog. sect. B , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 36
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 38
    • 0028301445 scopus 로고
    • Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
    • Mitchell J.B., Nandi C.L., McDonald I.K., Thornton J.M., and Price S.L. Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?. J. Mol. Biol. 239 (1994) 315-331
    • (1994) J. Mol. Biol. , vol.239 , pp. 315-331
    • Mitchell, J.B.1    Nandi, C.L.2    McDonald, I.K.3    Thornton, J.M.4    Price, S.L.5
  • 39
    • 0242417008 scopus 로고    scopus 로고
    • Interactions with aromatic rings in chemical and biological recognition
    • Meyer E.A., Castellano R.K., and Diederich F. Interactions with aromatic rings in chemical and biological recognition. Angew. Chem. Int. Ed Engl. 42 (2003) 1210-1250
    • (2003) Angew. Chem. Int. Ed Engl. , vol.42 , pp. 1210-1250
    • Meyer, E.A.1    Castellano, R.K.2    Diederich, F.3
  • 40
    • 0033668689 scopus 로고    scopus 로고
    • Predicting binding modes, binding affinities and "hot spots" for protein-ligand complexes using a knowledge-based scoring function
    • Gohlke H., Hendlich M., and Klebe G. Predicting binding modes, binding affinities and "hot spots" for protein-ligand complexes using a knowledge-based scoring function. Persp. Drug Des. Discov. 20 (2000) 115-144
    • (2000) Persp. Drug Des. Discov. , vol.20 , pp. 115-144
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 41
    • 0035312864 scopus 로고    scopus 로고
    • Statistical potentials and scoring functions applied to protein-ligand binding
    • Gohlke H., and Klebe G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol. 11 (2001) 231-235
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 231-235
    • Gohlke, H.1    Klebe, G.2
  • 42
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke H., Hendlich M., and Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 295 (2000) 337-356
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 44
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds. Binding site similarity in the absence of homology
    • Russell R.B., Sasieni P.D., and Sternberg M.J. Supersites within superfolds. Binding site similarity in the absence of homology. J. Mol. Biol. 282 (1998) 903-918
    • (1998) J. Mol. Biol. , vol.282 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.3
  • 45
    • 0004204457 scopus 로고    scopus 로고
    • An example of enzyme catalysis: serine proteases
    • Garland, New York (chapt. 11)
    • Branden C., and Tooze J. An example of enzyme catalysis: serine proteases. Introduction to Protein Structure. 2nd edit. (1999), Garland, New York 205-220 (chapt. 11)
    • (1999) Introduction to Protein Structure. 2nd edit. , pp. 205-220
    • Branden, C.1    Tooze, J.2
  • 46
    • 0029973830 scopus 로고    scopus 로고
    • Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
    • Wallace A.C., Laskowski R.A., and Thornton J.M. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5 (1996) 1001-1013
    • (1996) Protein Sci. , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 47
    • 0029921058 scopus 로고    scopus 로고
    • Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism
    • Thoden J.B., Frey P.A., and Holden H.M. Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism. Biochemistry 35 (1996) 5137-5144
    • (1996) Biochemistry , vol.35 , pp. 5137-5144
    • Thoden, J.B.1    Frey, P.A.2    Holden, H.M.3
  • 48
    • 0035783055 scopus 로고    scopus 로고
    • On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
    • Lupas A.N., Ponting C.P., and Russell R.B. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?. J. Struct. Biol. 134 (2001) 191-203
    • (2001) J. Struct. Biol. , vol.134 , pp. 191-203
    • Lupas, A.N.1    Ponting, C.P.2    Russell, R.B.3
  • 50
    • 0042198682 scopus 로고    scopus 로고
    • Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome
    • Kuiken T., Fouchier R.A., Schutten M., Rimmelzwaan G.F., Amerongen G.v., Riel D.v., et al. Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome. Lancet 362 (2003) 263-270
    • (2003) Lancet , vol.362 , pp. 263-270
    • Kuiken, T.1    Fouchier, R.A.2    Schutten, M.3    Rimmelzwaan, G.F.4    Amerongen, G.v.5    Riel, D.v.6
  • 51
    • 0034072633 scopus 로고    scopus 로고
    • Virus-encoded proteinases and proteolytic processing in the Nidovirales
    • Ziebuhr J., Snijder E.J., and Gorbalenya A.E. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J. Gen. Virol. 81 (2000) 853-879
    • (2000) J. Gen. Virol. , vol.81 , pp. 853-879
    • Ziebuhr, J.1    Snijder, E.J.2    Gorbalenya, A.E.3
  • 52
    • 0036646055 scopus 로고    scopus 로고
    • Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain
    • Anand K., Palm G.J., Mesters J.R., Siddell S.G., Ziebuhr J., and Hilgenfeld R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J. 21 (2002) 3213-3224
    • (2002) EMBO J. , vol.21 , pp. 3213-3224
    • Anand, K.1    Palm, G.J.2    Mesters, J.R.3    Siddell, S.G.4    Ziebuhr, J.5    Hilgenfeld, R.6
  • 53
    • 0038120984 scopus 로고    scopus 로고
    • Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs
    • Anand K., Ziebuhr J., Wadhwani P., Mesters J.R., and Hilgenfeld R. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science 300 (2003) 1763-1767
    • (2003) Science , vol.300 , pp. 1763-1767
    • Anand, K.1    Ziebuhr, J.2    Wadhwani, P.3    Mesters, J.R.4    Hilgenfeld, R.5
  • 54
    • 0345255626 scopus 로고    scopus 로고
    • The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor
    • Yang H., Yang M., Ding Y., Liu Y., Lou Z., Zhou Z., et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl Acad. Sci. USA 100 (2003) 13190-13195
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13190-13195
    • Yang, H.1    Yang, M.2    Ding, Y.3    Liu, Y.4    Lou, Z.5    Zhou, Z.6
  • 55
    • 13044300859 scopus 로고    scopus 로고
    • Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes
    • Matthews D.A., Dragovich P.S., Webber S.E., Fuhrman S.A., Patick A.K., Zalman L.S., et al. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc. Natl Acad. Sci. USA 96 (1999) 11000-11007
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11000-11007
    • Matthews, D.A.1    Dragovich, P.S.2    Webber, S.E.3    Fuhrman, S.A.4    Patick, A.K.5    Zalman, L.S.6
  • 56
    • 0033535596 scopus 로고    scopus 로고
    • Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 4. Incorporation of P1 lactam moieties as l-glutamine replacements
    • Dragovich P.S., Prins T.J., Zhou R., Webber S.E., Marakovits J.T., Fuhrman S.A., et al. Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 4. Incorporation of P1 lactam moieties as l-glutamine replacements. J. Med. Chem. 42 (1999) 1213-1224
    • (1999) J. Med. Chem. , vol.42 , pp. 1213-1224
    • Dragovich, P.S.1    Prins, T.J.2    Zhou, R.3    Webber, S.E.4    Marakovits, J.T.5    Fuhrman, S.A.6
  • 57
    • 22844437876 scopus 로고    scopus 로고
    • Inhibition of the severe acute respiratory syndrome 3CL protease by peptidomimetic alpha,beta-unsaturated esters
    • Shie J.J., Fang J.M., Kuo T.H., Kuo C.J., Liang P.H., Huang H.J., et al. Inhibition of the severe acute respiratory syndrome 3CL protease by peptidomimetic alpha,beta-unsaturated esters. Bioorg. Med. Chem. 13 (2005) 5240-5252
    • (2005) Bioorg. Med. Chem. , vol.13 , pp. 5240-5252
    • Shie, J.J.1    Fang, J.M.2    Kuo, T.H.3    Kuo, C.J.4    Liang, P.H.5    Huang, H.J.6
  • 58
    • 26444498493 scopus 로고    scopus 로고
    • Design of wide-spectrum inhibitors targeting coronavirus main proteases
    • Yang H., Xie W., Xue X., Yang K., Ma J., Liang W., et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS. Biol. 3 (2005) e324
    • (2005) PLoS. Biol. , vol.3
    • Yang, H.1    Xie, W.2    Xue, X.3    Yang, K.4    Ma, J.5    Liang, W.6
  • 59
    • 0030849266 scopus 로고    scopus 로고
    • Structure and mechanism of carbonic anhydrase
    • Lindskog S. Structure and mechanism of carbonic anhydrase. Pharmacol. Ther. 74 (1997) 1-20
    • (1997) Pharmacol. Ther. , vol.74 , pp. 1-20
    • Lindskog, S.1
  • 60
    • 0037075147 scopus 로고    scopus 로고
    • Structural aspects of isozyme selectivity in the binding of inhibitors to carbonic anhydrases II and IV
    • Kim C.Y., Whittington D.A., Chang J.S., Liao J., May J.A., and Christianson D.W. Structural aspects of isozyme selectivity in the binding of inhibitors to carbonic anhydrases II and IV. J. Med. Chem. 45 (2002) 888-893
    • (2002) J. Med. Chem. , vol.45 , pp. 888-893
    • Kim, C.Y.1    Whittington, D.A.2    Chang, J.S.3    Liao, J.4    May, J.A.5    Christianson, D.W.6
  • 62
    • 4444353636 scopus 로고    scopus 로고
    • Regulation of protein kinases; controlling activity through activation segment conformation
    • Nolen B., Taylor S., and Ghosh G. Regulation of protein kinases; controlling activity through activation segment conformation. Mol. Cell 15 (2004) 661-675
    • (2004) Mol. Cell , vol.15 , pp. 661-675
    • Nolen, B.1    Taylor, S.2    Ghosh, G.3
  • 63
    • 0035990907 scopus 로고    scopus 로고
    • Structural aspects of protein kinase control-role of conformational flexibility
    • Engh R.A., and Bossemeyer D. Structural aspects of protein kinase control-role of conformational flexibility. Pharmacol. Ther. 93 (2002) 99-111
    • (2002) Pharmacol. Ther. , vol.93 , pp. 99-111
    • Engh, R.A.1    Bossemeyer, D.2
  • 64
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • Huse M., and Kuriyan J. The conformational plasticity of protein kinases. Cell 109 (2002) 275-282
    • (2002) Cell , vol.109 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 65
    • 3342918498 scopus 로고    scopus 로고
    • The p38 MAP kinase pathway as a therapeutic target in inflammatory disease
    • Saklatvala J. The p38 MAP kinase pathway as a therapeutic target in inflammatory disease. Curr. Opin. Pharmacol. 4 (2004) 372-377
    • (2004) Curr. Opin. Pharmacol. , vol.4 , pp. 372-377
    • Saklatvala, J.1
  • 66
    • 0035479234 scopus 로고    scopus 로고
    • Tumor angiogenesis as a therapeutic target
    • Matter A. Tumor angiogenesis as a therapeutic target. Drug Discov. Today 6 (2001) 1005-1024
    • (2001) Drug Discov. Today , vol.6 , pp. 1005-1024
    • Matter, A.1
  • 67
    • 0037392444 scopus 로고    scopus 로고
    • Issues and progress with protein kinase inhibitors for cancer treatment
    • Dancey J., and Sausville E.A. Issues and progress with protein kinase inhibitors for cancer treatment. Nature Rev. Drug Discov. 2 (2003) 296-313
    • (2003) Nature Rev. Drug Discov. , vol.2 , pp. 296-313
    • Dancey, J.1    Sausville, E.A.2
  • 68
    • 0036527429 scopus 로고    scopus 로고
    • Protein kinases-the major drug targets of the twenty-first century?
    • Cohen P. Protein kinases-the major drug targets of the twenty-first century?. Nature Rev. Drug Discov. 1 (2002) 309-315
    • (2002) Nature Rev. Drug Discov. , vol.1 , pp. 309-315
    • Cohen, P.1
  • 69
    • 0031731295 scopus 로고    scopus 로고
    • Tyrosine kinase inhibitors in cancer treatment (part II)
    • Traxler P.M. Tyrosine kinase inhibitors in cancer treatment (part II). Exp. Opin. Ther. Patents 8 (1998) 1599-1625
    • (1998) Exp. Opin. Ther. Patents , vol.8 , pp. 1599-1625
    • Traxler, P.M.1
  • 70
    • 1642323740 scopus 로고    scopus 로고
    • Protein kinase inhibitors: insights into drug design from structure
    • Noble M.E., Endicott J.A., and Johnson L.N. Protein kinase inhibitors: insights into drug design from structure. Science 303 (2004) 1800-1805
    • (2004) Science , vol.303 , pp. 1800-1805
    • Noble, M.E.1    Endicott, J.A.2    Johnson, L.N.3
  • 71
    • 0037030707 scopus 로고    scopus 로고
    • Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: target family landscapes
    • Naumann T., and Matter H. Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: target family landscapes. J. Med. Chem. 45 (2002) 2366-2378
    • (2002) J. Med. Chem. , vol.45 , pp. 2366-2378
    • Naumann, T.1    Matter, H.2
  • 72
    • 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., and 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
  • 73
    • 0032214649 scopus 로고    scopus 로고
    • Databases for protein-ligand complexes
    • Hendlich M. Databases for protein-ligand complexes. Acta Crystallog. sect. D 54 (1998) 1178-1182
    • (1998) Acta Crystallog. sect. D , vol.54 , pp. 1178-1182
    • Hendlich, M.1
  • 74
    • 0037436339 scopus 로고    scopus 로고
    • Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions
    • Hendlich M., Bergner A., Günther J., and Klebe G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J. Mol. Biol. 326 (2003) 607-620
    • (2003) J. Mol. Biol. , vol.326 , pp. 607-620
    • Hendlich, M.1    Bergner, A.2    Günther, J.3    Klebe, G.4
  • 75
    • 0037436333 scopus 로고    scopus 로고
    • Utilising structural knowledge in drug design strategies: applications using Relibase
    • Gunther J., Bergner A., Hendlich M., and Klebe G. Utilising structural knowledge in drug design strategies: applications using Relibase. J. Mol. Biol. 326 (2003) 621-636
    • (2003) J. Mol. Biol. , vol.326 , pp. 621-636
    • Gunther, J.1    Bergner, A.2    Hendlich, M.3    Klebe, G.4
  • 76
    • 33744931936 scopus 로고    scopus 로고
    • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich M., Rippmann F., and Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model 359-63 (1997) 389
    • (1997) J. Mol. Graph. Model , vol.359-63 , pp. 389
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 77
    • 84976668743 scopus 로고
    • Algorithm 457. Finding all cliques of an undirected graph
    • Bron C., and Kerbosch J. Algorithm 457. Finding all cliques of an undirected graph. Commun. ACM 16 (1973) 575-577
    • (1973) Commun. ACM , vol.16 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 78
    • 0033643235 scopus 로고    scopus 로고
    • Searching for molecules with similar biological activity: analysis by fingerprint profiling
    • Godden J.W., Xue L., Stahura F.L., and Bajorath J. Searching for molecules with similar biological activity: analysis by fingerprint profiling. Pac. Symp. Biocomput. (2000) 566-575
    • (2000) Pac. Symp. Biocomput. , pp. 566-575
    • Godden, J.W.1    Xue, L.2    Stahura, F.L.3    Bajorath, J.4
  • 79
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • Bairoch A. The ENZYME database in 2000. Nucl. Acids Res 28 (2000) 304-305
    • (2000) Nucl. Acids Res , vol.28 , pp. 304-305
    • Bairoch, A.1
  • 83
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85 (1988) 2444-2448
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 84
    • 33745906224 scopus 로고    scopus 로고
    • Al-Gharabli, S.I., Shah, S.T.A., Weik, S., Schmidt, B.M.F., Mesters, J.R., Kuhn, D. et al. (2006). An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS corona virus main protease (SARS-CoV Mpro) inhibitors. Chem Bio Chem, in press.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.