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Volumn 6, Issue 3, 2014, Pages 319-331

Exploiting structural information for drug-target assessment

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84895469259     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc.14.3     Document Type: Review
Times cited : (25)

References (98)
  • 1
    • 77649234756 scopus 로고    scopus 로고
    • How to improve R&D productivity: The pharmaceutical industry's grand challenge
    • SM Paul, Mytelka DS, Dunwiddie TC et al. How to improve R&D productivity: The pharmaceutical industry's grand challenge. Nat. Rev. Drug Discov. 9(3), 203-214 (2010).
    • (2010) Nat. Rev. Drug Discov. , vol.9 , Issue.3 , pp. 203-214
    • Paul, S.M.1    Mytelka, D.S.2    Dunwiddie, T.C.3
  • 3
    • 70349318376 scopus 로고    scopus 로고
    • Structure is three to ten times more conserved than sequence-A study of structural response in protein cores
    • Illergard K, Ardell HD, Elofison A. Structure is three to ten times more conserved than sequence-A study of structural response in protein cores. Proteins 77(3), 499-508 (2009).
    • (2009) Proteins , vol.77 , Issue.3 , pp. 499-508
    • Illergard, K.1    Ardell, H.D.2    Elofison, A.3
  • 4
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman MH, Westbrook JZ, Feng et al. The protein data bank. Nucleic Acids Res. 28(1), 235-242 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , Issue.1 , pp. 235-242
    • Berman, M.H.1    Feng, W.J.Z.2
  • 5
    • 77950342398 scopus 로고    scopus 로고
    • An overview of in silico protein function prediction
    • Sleator RD, Walsh P. An overview of in silico protein function prediction. Arch Microbiol. 192(3), 151-155 (2010).
    • (2010) Arch Microbiol. , vol.192 , Issue.3 , pp. 151-155
    • Sleator, R.D.1    Walsh, P.2
  • 6
    • 79957979204 scopus 로고    scopus 로고
    • Comparative modeling: The state of the art and protein drug target structure prediction
    • Liu T, Tang GW, Capriotti E. Comparative modeling: The state of the art and protein drug target structure prediction. Comb. Chem. High Throughput Screen. 14(6), 532-547 (2011).
    • (2011) Comb. Chem. High Throughput Screen. , vol.14 , Issue.6 , pp. 532-547
    • Liu, T.1    Tang, G.W.2    Capriotti, E.3
  • 7
    • 76649139794 scopus 로고    scopus 로고
    • Computational approaches to identifying and characterizing protein binding sites for ligand design
    • Henrich SM, Salo-Ahen OB. Huang et al. Computational approaches to identifying and characterizing protein binding sites for ligand design. J. Mol. Recognit. 23(2), 209-219 (2010).
    • (2010) J. Mol. Recognit. , vol.23 , Issue.2 , pp. 209-219
    • Henrich, S.M.1    Salo-Ahen, O.B.H.2
  • 8
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Sci. 7(9), 1884-1897 (1998).
    • (1998) Protein Sci. , vol.7 , Issue.9 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 9
    • 42949151886 scopus 로고    scopus 로고
    • A structural biology view of target drugability
    • Egner U, Hillig RC. A structural biology view of target drugability. Expert Opin. Drug Discov. 3(4), 391-401 (2008).
    • (2008) Expert Opin. Drug Discov. , vol.3 , Issue.4 , pp. 391-401
    • Egner, U.1    Hillig, R.C.2
  • 11
    • 79953703975 scopus 로고    scopus 로고
    • Fragment screening to predict druggability (ligandability) and lead discovery success
    • Edfeldt FN, Folmer RH, Breeze AL. Fragment screening to predict druggability (ligandability) and lead discovery success. Drug Discov. Today 16(7-8), 284-287 (2011).
    • (2011) Drug Discov. Today , vol.16 , Issue.7-8 , pp. 284-287
    • Edfeldt, F.N.1    Folmer, R.H.2    Breeze, A.L.3
  • 12
    • 78649523910 scopus 로고    scopus 로고
    • Drug-like density: A method of quantifying the 'bindability' of a protein target based on a very large set of pockets and drug-like ligands from the protein data bank
    • Sheridan RP, Maiorov VN, Holloway MK et al. Drug-like density: A method of quantifying the 'bindability' of a protein target based on a very large set of pockets and drug-like ligands from the protein data bank. J. Chem. Inf. Model. 50(11), 2029-2040 (2010).
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.11 , pp. 2029-2040
    • Sheridan, R.P.1    Maiorov, V.N.2    Holloway, M.K.3
  • 13
    • 79951774159 scopus 로고    scopus 로고
    • Using protein-ligand docking to assess the chemical tractability of inhibiting a protein target
    • Ward RA. Using protein-ligand docking to assess the chemical tractability of inhibiting a protein target. J. Mol. Model. 16(12), 1833-1843 (2010).
    • (2010) J. Mol. Model. , vol.16 , Issue.12 , pp. 1833-1843
    • Ward, R.A.1
  • 15
    • 84879082760 scopus 로고    scopus 로고
    • Druggability predictions: Methods, limitations, and applications
    • Barril X. Druggability predictions: Methods, limitations, and applications. Wiley Interdiscip. Rev. Comput. Mol. Sci. 3(4), 327-338 (2013).
    • (2013) Wiley Interdiscip Rev. Comput. Mol. Sci. , vol.3 , Issue.4 , pp. 327-338
    • Barril, X.1
  • 16
    • 33846155913 scopus 로고    scopus 로고
    • Structure-based maximal affinity model predicts small-molecule druggability
    • Cheng AC, Coleman RG, Smyth KT et al. Structure-based maximal affinity model predicts small-molecule druggability. Nat. Biotechnol. 25(1), 71-75 (2007).
    • (2007) Nat. Biotechnol. , vol.25 , Issue.1 , pp. 71-75
    • Cheng, A.C.1    Coleman, R.G.2    Smyth, K.T.3
  • 17
    • 0842274205 scopus 로고    scopus 로고
    • Rediscovering the sweet spot in drug discovery
    • Brown D, Superti-Furga G. Rediscovering the sweet spot in drug discovery. Drug Discov. Today 8(23), 1067-1077 (2003).
    • (2003) Drug Discov. Today , vol.8 , Issue.23 , pp. 1067-1077
    • Brown, D.1    Superti-Furga, G.2
  • 18
    • 84873091814 scopus 로고    scopus 로고
    • Predicting enzymatic function from global binding site descriptors
    • Volkamer A, Kuhn D, Rippmann F, Rarey M. Predicting enzymatic function from global binding site descriptors. Proteins 81(3), 479-489 (2013).
    • (2013) Proteins , vol.81 , Issue.3 , pp. 479-489
    • Volkamer, A.1    Kuhn, D.2    Rippmann, F.3    Rarey, M.4
  • 19
    • 84879269767 scopus 로고    scopus 로고
    • Drug promiscuity in PDB: Protein binding site similarity is key
    • Haupt JV, Daminelli S, Schroeder M. Drug promiscuity in PDB: Protein binding site similarity is key. PLoS ONE 8(6), e65894 (2013).
    • (2013) PLoS ONE , vol.8 , Issue.6
    • Haupt, J.V.1    Daminelli, S.2    Schroeder, M.3
  • 20
    • 36949009488 scopus 로고    scopus 로고
    • In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
    • Xie L, Wang J, Bourne PE. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput. Biol. 3(11), e217 (2007).
    • (2007) PLoS Comput. Biol. , vol.3 , Issue.11
    • Xie, L.1    Wang, J.2    Bourne, P.E.3
  • 21
    • 68249144628 scopus 로고    scopus 로고
    • Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
    • Kinnings SL, Liu N, Buchmeier N et al. Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput. Biol. 5(7), e1000423 (2009).
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.7
    • Kinnings, S.L.1    Liu, N.2    Buchmeier, N.3
  • 22
    • 54749109580 scopus 로고    scopus 로고
    • How to measure the similarity between protein ligand-binding sites?
    • Kellenberger E, Schalon C, Rognan D. How to measure the similarity between protein ligand-binding sites? Curr. Comput. Aided Drug Des. 4(3), 209-220 (2008).
    • (2008) Curr Comput. Aided Drug Des. , vol.4 , Issue.3 , pp. 209-220
    • Kellenberger, E.1    Schalon, C.2    Rognan, D.3
  • 23
    • 78649499434 scopus 로고    scopus 로고
    • Analyzing the topology of active sites: On the prediction of pockets and subpockets
    • Volkamer A, Griewel A, Grombacher T, Rarey M. Analyzing the topology of active sites: On the prediction of pockets and subpockets. J. Chem. Inf. Model. 50(11), 2041-2052 (2010).
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.11 , pp. 2041-2052
    • Volkamer, A.1    Griewel, A.2    Grombacher, T.3    Rarey, M.4
  • 24
    • 0027053611 scopus 로고
    • Pocket: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • Levitt DG, Banaszak LJ. Pocket: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph. 10(4), 229-234 (1992).
    • (1992) J. Mol. Graph. , vol.10 , Issue.4 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 25
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich M, Rippmann F, Barnickel G. LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model. 15(6), 359-363 (1997).
    • (1997) J. Mol. Graph. Model. , vol.15 , Issue.6 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 26
    • 34547341277 scopus 로고    scopus 로고
    • PocketPicker: Analysis of ligand binding-sites with shape descriptors
    • Weisel M, Proschak E, Schneider G. PocketPicker: Analysis of ligand binding-sites with shape descriptors. Chem. Cent. J. 1, 7 (2007).
    • (2007) Chem. Cent. J. , vol.1 , pp. 7
    • Weisel, M.1    Proschak, E.2    Schneider, G.3
  • 27
    • 65249117514 scopus 로고    scopus 로고
    • Identifying and characterizing binding sites and assessing druggability
    • Halgren TA. Identifying and characterizing binding sites and assessing druggability. J. Chem. Inf. Model. 49(2), 377-389 (2009).
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.2 , pp. 377-389
    • Halgren, T.A.1
  • 28
    • 0028881975 scopus 로고
    • Surfnet: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski RA. Surfnet: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 13(5), 323-330 (1995).
    • (1995) J. Mol. Graph. , vol.13 , Issue.5 , pp. 323-330
    • Laskowski, R.A.1
  • 29
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with pass
    • Brady GPJ, Stouten PF. Fast prediction and visualization of protein binding pockets with pass. J. Comput. Aided Mol. Des. 14(4), 383-401 (2000).
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , Issue.4 , pp. 383-401
    • Brady, G.P.J.1    Stouten, P.F.2
  • 30
    • 0029935202 scopus 로고    scopus 로고
    • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
    • Peters KP, Fauck J, Frommel C. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J. Mol. Biol. 256(1), 201-213 (1996).
    • (1996) J. Mol. Biol. , vol.256 , Issue.1 , pp. 201-213
    • Peters, K.P.1    Fauck, J.2    Frommel, C.3
  • 31
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: An open source platform for ligand pocket detection
    • Le Guilloux V, Schmidtke P, Tuffery P. Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics 10, 168 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 32
    • 29144482496 scopus 로고    scopus 로고
    • Comprehensive identification of 'druggable' protein ligand binding sites
    • An J, Totrov M, Abagyan R. Comprehensive identification of 'druggable' protein ligand binding sites. Genome Inform. 15(2), 31-41 (2004).
    • (2004) Genome Inform. , vol.15 , Issue.2 , pp. 31-41
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 33
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • Laurie ATR, Jackson RM. Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21(9), 1908-1916 (2005).
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 34
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITECSC: Predicting ligand binding sites using the connolly surface and degree of conservation
    • Huang B, Schroeder M. LIGSITECSC: Predicting ligand binding sites using the connolly surface and degree of conservation. BMC Struct. Biol. 6, 19 (2006).
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 35
    • 30144442036 scopus 로고    scopus 로고
    • A method for localizing ligand binding pockets in protein structures
    • Glaser FJ, Morris R, Najmanovich RJ et al. A method for localizing ligand binding pockets in protein structures. Proteins 62(2), 479-488 (2006).
    • (2006) Proteins , vol.62 , Issue.2 , pp. 479-488
    • Glaser, F.J.1    Morris, R.2    Najmanovich, R.J.3
  • 36
    • 67449108422 scopus 로고    scopus 로고
    • Findsite: A combined evolution/structure-based approach to protein function prediction
    • Skolnick J, Brylinski M. Findsite: A combined evolution/structure-based approach to protein function prediction. Brief Bioinform. 10(4), 378-391 (2009).
    • (2009) Brief Bioinform. , vol.10 , Issue.4 , pp. 378-391
    • Skolnick, J.1    Brylinski, M.2
  • 37
    • 79960395595 scopus 로고    scopus 로고
    • Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
    • Zhang Z, Li Y, Lin B et al. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics 27(15), 2083-2088 (2011).
    • (2011) Bioinformatics , vol.27 , Issue.15 , pp. 2083-2088
    • Zhang, Z.1    Li, Y.2    Lin, B.3
  • 38
    • 77951217659 scopus 로고    scopus 로고
    • Detection of multiscale pockets on protein surfaces using mathematical morphology
    • Kawabata T. Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins 78(5), 1195-1211 (2010).
    • (2010) Proteins , vol.78 , Issue.5 , pp. 1195-1211
    • Kawabata, T.1
  • 39
    • 75249088440 scopus 로고    scopus 로고
    • Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
    • Yu J, Zhou Y, Tanaka I, Yao M. Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics 26(1), 46-52 2010.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 46-52
    • Yu, J.1    Zhou, Y.2    Tanaka, I.3    Yao, M.4
  • 40
    • 84863529885 scopus 로고    scopus 로고
    • Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
    • Xie RZ, Hwang MJ. Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles. Bioinformatics 28(12), 1579-1585 (2012).
    • (2012) Bioinformatics , vol.28 , Issue.12 , pp. 1579-1585
    • Xie, R.Z.1    Hwang, M.J.2
  • 41
    • 84873040004 scopus 로고    scopus 로고
    • Subpocket analysis method for fragment-based drug discovery
    • Kalliokoski T, Olsson TS, Vulpetti A. Subpocket analysis method for fragment-based drug discovery. J. Chem. Inf. Model. 53(1), 131-141 (2013).
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.1 , pp. 131-141
    • Kalliokoski, T.1    Olsson, T.S.2    Vulpetti, A.3
  • 42
    • 82255164267 scopus 로고    scopus 로고
    • MDpocket: Open-source cavity detection and characterization on molecular dynamics trajectories
    • Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X. MDpocket: Open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics 27(23), 3276-3285 (2011).
    • (2011) Bioinformatics , vol.27 , Issue.23 , pp. 3276-3285
    • Schmidtke, P.1    Bidon-Chanal, A.2    Luque, F.J.3    Barril, X.4
  • 43
    • 80054928519 scopus 로고    scopus 로고
    • Pocket-space maps to identify novel binding-site conformations in proteins
    • Craig IR, Pfleger C, Gohlke H et al. Pocket-space maps to identify novel binding-site conformations in proteins. J. Chem. Inf. Model. 51(10), 2666-2679 (2011).
    • (2011) J. Chem. Inf. Model. , vol.51 , Issue.10 , pp. 2666-2679
    • Craig, I.R.1    Pfleger, C.2    Gohlke, H.3
  • 44
    • 84878181372 scopus 로고    scopus 로고
    • TRAPP: A tool for analysis of transient binding pockets in proteins
    • Kokh DB, Richter S, Henrich S et al. TRAPP: A tool for analysis of transient binding pockets in proteins. J. Chem. Inf. Model. 53(5), 1235-1252 (2013).
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.5 , pp. 1235-1252
    • Kokh, D.B.1    Richter, S.2    Henrich, S.3
  • 46
    • 17144373303 scopus 로고    scopus 로고
    • Druggability indices for protein targets derived from NMR-based screening data
    • Hajduk PJ, Huth JR, Fesik SW. Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 48(7), 2518-2525 (2005).
    • (2005) J. Med. Chem. , vol.48 , Issue.7 , pp. 2518-2525
    • Hajduk, P.J.1    Huth, J.R.2    Fesik, S.W.3
  • 48
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites
    • Nayal M, Honig B. On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites. Proteins 63(4), 892-906 (2006).
    • (2006) Proteins , vol.63 , Issue.4 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 49
    • 60349119258 scopus 로고    scopus 로고
    • Form follows function: Shape analysis of protein cavities for receptor-based drug design
    • Weisel M, Proschak E, Kriegl JM, Schneider G. Form follows function: Shape analysis of protein cavities for receptor-based drug design. Proteomics 9(2), 451-459 (2009).
    • (2009) Proteomics , vol.9 , Issue.2 , pp. 451-459
    • Weisel, M.1    Proschak, E.2    Kriegl, J.M.3    Schneider, G.4
  • 50
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • Wang R, Fang X, Lu Y, Wang S. The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 47(12), 2977-2980 (2004).
    • (2004) J. Med. Chem. , vol.47 , Issue.12 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 51
    • 82355186340 scopus 로고    scopus 로고
    • DrugPred: A structure-based approach to predict protein druggability developed using an extensive nonredundant data set
    • Krasowski A, Muthas D, A. Sarkar et al. DrugPred: A structure-based approach to predict protein druggability developed using an extensive nonredundant data set. J. Chem. Inf. Model. 51(11), 2829-2842 (2011).
    • (2011) J. Chem. Inf. Model. , vol.51 , Issue.11 , pp. 2829-2842
    • Krasowski, A.1    Muthas, D.2    Sarkar, A.3
  • 52
    • 77955397914 scopus 로고    scopus 로고
    • Understanding and predicting druggability A high-Throughput method for detection of drug binding sites
    • Schmidtke P, Barril X. Understanding and predicting druggability. A high-Throughput method for detection of drug binding sites. J. Med. Chem. 53(15), 5858-5867 (2010).
    • (2010) J. Med. Chem. , vol.53 , Issue.15 , pp. 5858-5867
    • Schmidtke, P.1    Barril, X.2
  • 53
    • 84857531280 scopus 로고    scopus 로고
    • Combining global and local measures for structure-based druggability predictions
    • Volkamer A, Kuhn D, Grombacher T, Rippmann F, Rarey M. Combining global and local measures for structure-based druggability predictions. J. Chem. Inf. Model. 52(2), 360-372 (2012).
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.2 , pp. 360-372
    • Volkamer, A.1    Kuhn, D.2    Grombacher, T.3    Rippmann, F.4    Rarey, M.5
  • 54
    • 84862000655 scopus 로고    scopus 로고
    • Development of a rule-based method for the assessment of protein druggability
    • Perola E, Herman L, Weiss J. Development of a rule-based method for the assessment of protein druggability. J. Chem. Inf. Model. 52(4), 1027-38 (2012).
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.4 , pp. 1027-1038
    • Perola, E.1    Herman, L.2    Weiss, J.3
  • 55
    • 33746076877 scopus 로고    scopus 로고
    • Effects of conformational dynamics on predicted protein druggability
    • Brown PS, Hajduk PJ. Effects of conformational dynamics on predicted protein druggability. ChemMedChem. 1(1), 70-72 (2006).
    • (2006) Chem Med Chem. , vol.1 , Issue.1 , pp. 70-72
    • Brown, P.S.1    Hajduk, P.J.2
  • 57
    • 0030777303 scopus 로고    scopus 로고
    • CATH-A hierarchic classification of protein domain structures
    • Orengo CA, Michie AD, Jones S et al. CATH-A hierarchic classification of protein domain structures. Structure 5(8), 1093-1109 (1997).
    • (1997) Structure , vol.5 , Issue.8 , pp. 1093-1109
    • Orengo, C.A.1    Michie, A.D.2    Jones, S.3
  • 60
    • 77950855514 scopus 로고    scopus 로고
    • Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: Implications for classification of enzyme function
    • Almonacid DE, Yera ER, Mitchell JB, Babbitt PC. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: Implications for classification of enzyme function. PLoS Comput. Biol. 6(3), e1000700 (2010).
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.3
    • Almonacid, D.E.1    Yera, E.R.2    Mitchell, J.B.3    Babbitt, P.C.4
  • 61
    • 44949110143 scopus 로고    scopus 로고
    • Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
    • Minai R, Matsuo Y, Onuki H, Hirota H. Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins 72(1), 367-381 (2008).
    • (2008) Proteins , vol.72 , Issue.1 , pp. 367-381
    • Minai, R.1    Matsuo, Y.2    Onuki, H.3    Hirota, H.4
  • 62
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3d sites in protein structures
    • Jambon M, Imberty A, Deleage G, Geourjon C. A new bioinformatic approach to detect common 3d sites in protein structures. Proteins 52(2), 137-145 (2003).
    • (2003) Proteins , vol.52 , Issue.2 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deleage, G.3    Geourjon, C.4
  • 63
    • 3042809615 scopus 로고    scopus 로고
    • Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-Against-All structural comparison using geometric matching
    • Brakoulias A, Jackson RM. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-Against-All structural comparison using geometric matching. Proteins 56(2), 250-260 (2004).
    • (2004) Proteins , vol.56 , Issue.2 , pp. 250-260
    • Brakoulias, A.1    Jackson, R.M.2
  • 64
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. J. Mol. Biol. 339(3), 607-633 (2004).
    • (2004) J. Mol. Biol. , vol.339 , Issue.3 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 65
    • 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 AC, Borkakoti N, Thornton JM. Tess: A geometric hashing algorithm for deriving 3d coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6(11), 2308-2323 (1997).
    • (1997) Protein Sci. , vol.6 , Issue.11 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 66
    • 0141482410 scopus 로고    scopus 로고
    • Common structural cliques: A tool for protein structure and function analysis
    • Milik M, Szalma S, Olszewski KA. Common structural cliques: A tool for protein structure and function analysis. Protein Eng. 16(8), 543-552 (2003).
    • (2003) Protein Eng. , vol.16 , Issue.8 , pp. 543-552
    • Milik, M.1    Szalma, S.2    Olszewski, K.A.3
  • 67
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt S, Kuhn D, Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 323(2), 387-406 (2002).
    • (2002) J. Mol. Biol. , vol.323 , Issue.2 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 68
    • 33744935012 scopus 로고    scopus 로고
    • From the similarity analysis of protein cavities to the functional classification of protein families using cavbase
    • Kuhn D, Weskamp N, Schmitt S, Huellermeier E, Klebe G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. J. Mol. Biol. 359(4), 1023-1044 (2006).
    • (2006) J. Mol. Biol. , vol.359 , Issue.4 , pp. 1023-1044
    • Kuhn, D.1    Weskamp, N.2    Schmitt, S.3    Huellermeier, E.4    Klebe, G.5
  • 69
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita K, Furui J, Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics 2(1), 9-22 (2002).
    • (2002) J. Struct. Funct. Genomics , vol.2 , Issue.1 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 70
    • 34547587452 scopus 로고    scopus 로고
    • EF-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    • Kinoshita K, Murakami Y, Nakamura H. eF-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res. 35, W398-W402 (2007).
    • (2007) Nucleic Acids Res. , vol.35
    • Kinoshita, K.1    Murakami, Y.2    Nakamura, H.3
  • 71
    • 49649083383 scopus 로고    scopus 로고
    • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    • Najmanovich R, Kurbatova N, Thornton J. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics 24(16), i105-i111 (2008).
    • (2008) Bioinformatics , vol.24 , Issue.16
    • Najmanovich, R.1    Kurbatova, N.2    Thornton, J.3
  • 72
    • 84864485292 scopus 로고    scopus 로고
    • Probis-2012: Web server and web services for detection of structurally similar binding sites in proteins
    • Konc J, Janezic D. Probis-2012: Web server and web services for detection of structurally similar binding sites in proteins. Nucleic Acids Res. 40, W214-W221 (2012).
    • (2012) Nucleic Acids Res. , vol.40
    • Konc, J.1    Janezic, D.2
  • 73
    • 19544389524 scopus 로고    scopus 로고
    • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    • Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 21(10), 2347-2355 (2005).
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2347-2355
    • Morris, R.J.1    Najmanovich, R.J.2    Kahraman, A.3    Thornton, J.M.4
  • 74
    • 84864593192 scopus 로고    scopus 로고
    • Structure-And sequence-based function prediction for non-homologous proteins
    • Sael L, Chitale M, Kihara D. Structure-And sequence-based function prediction for non-homologous proteins. J. Struct. Funct. Genomics 13(2), 111-123 (2012).
    • (2012) J. Struct. Funct. Genomics , vol.13 , Issue.2 , pp. 111-123
    • Sael, L.1    Chitale, M.2    Kihara, D.3
  • 75
    • 60649117152 scopus 로고    scopus 로고
    • PocketMatch: A new algorithm to compare binding sites in protein structures
    • Yeturu K, Chandra N. PocketMatch: A new algorithm to compare binding sites in protein structures. BMC Bioinformatics 9, 543 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 543
    • Yeturu, K.1    Chandra, N.2
  • 76
    • 34247263219 scopus 로고    scopus 로고
    • A common reference framework for analyzing/comparing proteins and ligands fingerprints for ligands and proteins (FLAP): Theory and application
    • Baroni M, Cruciani G, Sciabola S, Perruccio F, Mason JS. A common reference framework for analyzing/comparing proteins and ligands fingerprints for ligands and proteins (FLAP): Theory and application. J. Chem. Inf. Model. 47(2), 279-294 (2007).
    • (2007) J. Chem. Inf. Model. , vol.47 , Issue.2 , pp. 279-294
    • Baroni, M.1    Cruciani, G.2    Sciabola, S.3    Perruccio, F.4    Mason, J.S.5
  • 77
    • 44349119204 scopus 로고    scopus 로고
    • A simple and fuzzy method to align and compare druggable ligand-binding sites
    • Schalon C, Surgand JS, Kellenberger E, Rognan D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins 71(4), 1755-1778 (2008).
    • (2008) Proteins , vol.71 , Issue.4 , pp. 1755-1778
    • Schalon, C.1    Surgand, J.S.2    Kellenberger, E.3    Rognan, D.4
  • 78
    • 75749155406 scopus 로고    scopus 로고
    • Alignment-free ultra-high-Throughput comparison of druggable protein-ligand binding sites
    • Weill N, Rognan D. Alignment-free ultra-high-Throughput comparison of druggable protein-ligand binding sites. J. Chem. Inf. Model. 50(1), 123-135 (2010).
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.1 , pp. 123-135
    • Weill, N.1    Rognan, D.2
  • 79
    • 84865503111 scopus 로고    scopus 로고
    • Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement
    • Wood DJ, De Vlieg J, Wagener M, Ritschel T. Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement. J. Chem Inf. Model. 52(8), 2031-2043 (2012).
    • (2012) J. Chem Inf. Model. , vol.52 , Issue.8 , pp. 2031-2043
    • Wood, D.J.1    De Vlieg, J.2    Wagener, M.3    Ritschel, T.4
  • 80
    • 67651242479 scopus 로고    scopus 로고
    • BSAlign: A rapid graph-based algorithm for detecting ligand-binding sites in protein structures
    • Aung Z, Tong JC. BSAlign: A rapid graph-based algorithm for detecting ligand-binding sites in protein structures. Genome Inform. 21, 65-76 (2008).
    • (2008) Genome Inform. , vol.21 , pp. 65-76
    • Aung, Z.1    Tong, J.C.2
  • 81
    • 84867997005 scopus 로고    scopus 로고
    • A fast algorithm for the maximum clique problem
    • Oestergaard PRJ. A fast algorithm for the maximum clique problem. Discrete Appl. Math. 120(1-3), 197-207 (2002).
    • (2002) Discrete Appl. Math. , vol.120 , Issue.1-3 , pp. 197-207
    • Oestergaard, P.R.J.1
  • 82
    • 84865516554 scopus 로고    scopus 로고
    • Comparison and druggability prediction of protein-ligand binding sites from pharmacophore-Annotated cavity shapes
    • Desaphy J, Azdimousa K, Kellenberger E, Rognan D. Comparison and druggability prediction of protein-ligand binding sites from pharmacophore-Annotated cavity shapes. J. Chem. Inf. Model. 52(8), 2287-2299 (2012).
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.8 , pp. 2287-2299
    • Desaphy, J.1    Azdimousa, K.2    Kellenberger, E.3    Rognan, D.4
  • 83
    • 84874447151 scopus 로고    scopus 로고
    • Fast protein binding site comparison via an index-based screening technology
    • Von Behren MM, Volkamer A, Henzler AM et al. Fast protein binding site comparison via an index-based screening technology. J. Chem. Inf. Model. 53(2), 411-422 (2013).
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.2 , pp. 411-422
    • Von Behren, M.M.1    Volkamer, A.2    Henzler, A.M.3
  • 84
    • 34548778124 scopus 로고    scopus 로고
    • A novel approach to local similarity of protein binding sites substantially improves computational drug design results
    • Ramensky V, Sobol A, Zaitseva N, Rubinov A, Zosimov V. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 69(2), 349-357 (2007).
    • (2007) Proteins , vol.69 , Issue.2 , pp. 349-357
    • Ramensky, V.1    Sobol, A.2    Zaitseva, N.3    Rubinov, A.4    Zosimov, V.5
  • 85
    • 65249116422 scopus 로고    scopus 로고
    • Computational fragment-based approach at PDB scale by protein local similarity
    • Moriaud F, Doppelt-Azeroual O, Martin L et al. Computational fragment-based approach at PDB scale by protein local similarity. J. Chem. Inf. Model. 49(2), 280-294 (2009).
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.2 , pp. 280-294
    • Moriaud, F.1    Doppelt-Azeroual, O.2    Martin, L.3
  • 86
    • 66349094968 scopus 로고    scopus 로고
    • Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
    • Wallach I, Lilien RH. Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. Bioinformatics 25(12), i296-i304 (2009).
    • (2009) Bioinformatics , vol.25 , Issue.12
    • Wallach, I.1    Lilien, R.H.2
  • 87
    • 84886950237 scopus 로고    scopus 로고
    • One hundred thousand mouse clicks down the road: Selected online resources supporting drug discovery collected over a decade
    • Villoutreix BO, Lagorce D, Labbé CM, Sperandio O, Miteva MA. One hundred thousand mouse clicks down the road: Selected online resources supporting drug discovery collected over a decade. Drug Discov. Today 18(21-22), 1081-1089 (2013).
    • (2013) Drug Discov. Today , vol.18 , Issue.21-22 , pp. 1081-1089
    • Villoutreix, B.O.1    Lagorce, D.2    Labbé, C.M.3    Sperandio, O.4    Miteva, M.A.5
  • 88
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (casp)-round ix
    • Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins 79(Suppl. 10), 1-5 (2011).
    • (2011) Proteins , vol.79 , Issue.10 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 89
    • 42649118439 scopus 로고    scopus 로고
    • Biological sequence classification utilizing positive and unlabeled data
    • Xiao Y, Segal MR. Biological sequence classification utilizing positive and unlabeled data. Bioinformatics 24(9), 1198-1205 (2008).
    • (2008) Bioinformatics , vol.24 , Issue.9 , pp. 1198-1205
    • Xiao, Y.1    Segal, M.R.2
  • 90
    • 84856211919 scopus 로고    scopus 로고
    • Virtual screening for compounds that mimic protein-protein interface epitopes
    • Geppert T, Reisen F, Pillong M et al. Virtual screening for compounds that mimic protein-protein interface epitopes. J. Comput. Chem. 33(5), 573-579 (2012).
    • (2012) J. Comput. Chem. , vol.33 , Issue.5 , pp. 573-579
    • Geppert, T.1    Reisen, F.2    Pillong, M.3
  • 91
    • 84877059094 scopus 로고    scopus 로고
    • Design of libraries targeting protein-protein interfaces
    • Fry D, Huang K, Di Lello P et al. Design of libraries targeting protein-protein interfaces. ChemMedChem 8(5), 726-732 (2013).
    • (2013) Chem Med Chem , vol.8 , Issue.5 , pp. 726-732
    • Fry, D.1    Huang, K.2    Di Lello, P.3
  • 92
    • 58849145512 scopus 로고    scopus 로고
    • Predicting druggable binding sites at the protein-protein interface
    • Fuller JC, Burgoyne NJ, Jackson RM. Predicting druggable binding sites at the protein-protein interface. Drug Discov. Today, 14(3-4), 155-161 (2009).
    • (2009) Drug Discov. Today , vol.14 , Issue.3-4 , pp. 155-161
    • Fuller, J.C.1    Burgoyne, N.J.2    Jackson, R.M.3
  • 93
    • 84865237493 scopus 로고    scopus 로고
    • Protein flexibility in docking and surface mapping
    • Lexa KW, Carlson HA. Protein flexibility in docking and surface mapping. Q. Rev. Biophys. 45(3), 301-343 (2012).
    • (2012) Q. Rev. Biophys. , vol.45 , Issue.3 , pp. 301-343
    • Lexa, K.W.1    Carlson, H.A.2
  • 95
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland ED. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl Acad. Sci. USA 44(2), 98-104 (1958).
    • (1958) Proc. Natl Acad. Sci. USA , vol.44 , Issue.2 , pp. 98-104
    • Koshland, E.D.1
  • 96
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • Shaw DE, Maragakis P, Lindorff-Larsen K et al. Atomic-level characterization of the structural dynamics of proteins. Science 330(6002), 341-346 (2010).
    • (2010) Science , vol.330 , Issue.6002 , pp. 341-346
    • Shaw, D.E.1    Maragakis, P.2    Lindorff-Larsen, K.3
  • 97
    • 34547583152 scopus 로고    scopus 로고
    • Transient pockets on protein surfaces involved in protein-protein interaction
    • Eyrisch S, Helms V. Transient pockets on protein surfaces involved in protein-protein interaction. J. Med. Chem. 50(15), 3457-3464 (2007).
    • (2007) J. Med. Chem. , vol.50 , Issue.15 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 98
    • 84887620421 scopus 로고    scopus 로고
    • Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
    • Dror RO, Green HF, Valant C et al. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature 503(7475), 295-299 (2013).
    • (2013) Nature , vol.503 , Issue.7475 , pp. 295-299
    • Dror, R.O.1    Green, H.F.2    Valant, C.3


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