메뉴 건너뛰기




Volumn 55, Issue 8, 2015, Pages 1585-1599

AlphaSpace: Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces

Author keywords

[No Author keywords available]

Indexed keywords

BIOMIMETICS; DRUG INTERACTIONS; MAPPING; MOLECULES;

EID: 84940200063     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00103     Document Type: Article
Times cited : (52)

References (93)
  • 1
    • 20444376940 scopus 로고    scopus 로고
    • Protein-Protein Interactions and Cancer: Small Molecules Going in for the Kill
    • Arkin, M. Protein-Protein Interactions and Cancer: Small Molecules Going in for the Kill Curr. Opin. Chem. Biol. 2005, 9, 317-324 10.1016/j.cbpa.2005.03.001
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 317-324
    • Arkin, M.1
  • 2
  • 5
    • 57649138736 scopus 로고    scopus 로고
    • Small Molecule Protein-Protein Interaction Inhibitors as CNS Therapeutic Agents: Current Progress and Future Hurdles
    • Blazer, L. L.; Neubig, R. R. Small Molecule Protein-Protein Interaction Inhibitors as CNS Therapeutic Agents: Current Progress and Future Hurdles Neuropsychopharmacology 2009, 34, 126-141 10.1038/npp.2008.151
    • (2009) Neuropsychopharmacology , vol.34 , pp. 126-141
    • Blazer, L.L.1    Neubig, R.R.2
  • 6
    • 80052168618 scopus 로고    scopus 로고
    • Dimeric MHC-Peptides Inserted into an Immunoglobulin Scaffold as New Immunotherapeutic Agents
    • Goldberg, B.; Bona, C. Dimeric MHC-Peptides Inserted into an Immunoglobulin Scaffold as New Immunotherapeutic Agents J. Cell. Mol. Med. 2011, 15, 1822-1832 10.1111/j.1582-4934.2011.01319.x
    • (2011) J. Cell. Mol. Med. , vol.15 , pp. 1822-1832
    • Goldberg, B.1    Bona, C.2
  • 10
    • 33847619355 scopus 로고    scopus 로고
    • Optimization and Determination of the Absolute Configuration of a Series of Potent Inhibitors of Human Papillomavirus Type-11 E1-E2 Protein-Protein Interaction: A Combined Medicinal Chemistry, NMR and Computational Chemistry Approach
    • Goudreau, N.; Cameron, D. R.; Déziel, R.; Haché, B.; Jakalian, A.; Malenfant, E.; Naud, J.; Ogilvie, W. W.; O'meara, J.; White, P. W.; Yoakim, C. Optimization and Determination of the Absolute Configuration of a Series of Potent Inhibitors of Human Papillomavirus Type-11 E1-E2 Protein-Protein Interaction: A Combined Medicinal Chemistry, NMR and Computational Chemistry Approach Bioorg. Med. Chem. 2007, 15, 2690-2700 10.1016/j.bmc.2007.01.036
    • (2007) Bioorg. Med. Chem. , vol.15 , pp. 2690-2700
    • Goudreau, N.1    Cameron, D.R.2    Déziel, R.3    Haché, B.4    Jakalian, A.5    Malenfant, E.6    Naud, J.7    Ogilvie, W.W.8    O'Meara, J.9    White, P.W.10    Yoakim, C.11
  • 12
    • 0034177264 scopus 로고    scopus 로고
    • Antagonists of Protein-Protein Interactions
    • Cochran, A. Antagonists of Protein-Protein Interactions Chem. Biol. 2000, 7, R85-R94 10.1016/S1074-5521(00)00106-X
    • (2000) Chem. Biol. , vol.7 , pp. 85-R94
    • Cochran, A.1
  • 13
    • 0032401982 scopus 로고    scopus 로고
    • High-Throughput Screening of Historic Collections: Observations on File Size, Biological Targets, and File Diversity
    • Spencer, R. W. High-Throughput Screening of Historic Collections: Observations on File Size, Biological Targets, and File Diversity Biotechnol. Bioeng. 1998, 61, 61-67 10.1002/(SICI)1097-0290(199824)61:1<61::AID-BIT11>3.0.CO;2-C
    • (1998) Biotechnol. Bioeng. , vol.61 , pp. 61-67
    • Spencer, R.W.1
  • 14
    • 33646567148 scopus 로고    scopus 로고
    • Between a Rock and a Hard Place?
    • Whitty, A.; Kumaravel, G. Between a Rock and a Hard Place? Nat. Chem. Biol. 2006, 2, 112-118 10.1038/nchembio0306-112
    • (2006) Nat. Chem. Biol. , vol.2 , pp. 112-118
    • Whitty, A.1    Kumaravel, G.2
  • 15
    • 33644839988 scopus 로고    scopus 로고
    • Diversity-Oriented Synthesis: Exploring the Intersections between Chemistry and Biology
    • Tan, D. S. Diversity-Oriented Synthesis: Exploring the Intersections between Chemistry and Biology Nat. Chem. Biol. 2005, 1, 74-84 10.1038/nchembio0705-74
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 74-84
    • Tan, D.S.1
  • 16
    • 84909587217 scopus 로고    scopus 로고
    • Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality
    • Arkin, M. R.; Tang, Y.; Wells, J. A. Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality Chem. Biol. 2014, 21, 1102-1114 10.1016/j.chembiol.2014.09.001
    • (2014) Chem. Biol. , vol.21 , pp. 1102-1114
    • Arkin, M.R.1    Tang, Y.2    Wells, J.A.3
  • 17
    • 84875436143 scopus 로고    scopus 로고
    • Inhibition of A-Helix-Mediated Protein-Protein Interactions Using Designed Molecules
    • Azzarito, V.; Long, K.; Murphy, N. S.; Wilson, A. J. Inhibition of A-Helix-Mediated Protein-Protein Interactions Using Designed Molecules Nat. Chem. 2013, 5, 161-173 10.1038/nchem.1568
    • (2013) Nat. Chem. , vol.5 , pp. 161-173
    • Azzarito, V.1    Long, K.2    Murphy, N.S.3    Wilson, A.J.4
  • 19
    • 67849113794 scopus 로고    scopus 로고
    • The Rise of Fragment-Based Drug Discovery
    • Murray, C. W.; Rees, D. C. The Rise of Fragment-Based Drug Discovery Nat. Chem. 2009, 1, 187-192 10.1038/nchem.217
    • (2009) Nat. Chem. , vol.1 , pp. 187-192
    • Murray, C.W.1    Rees, D.C.2
  • 20
    • 46849089254 scopus 로고    scopus 로고
    • Recent Developments in Fragment-Based Drug Discovery
    • Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent Developments in Fragment-Based Drug Discovery J. Med. Chem. 2008, 51, 3661-3680 10.1021/jm8000373
    • (2008) J. Med. Chem. , vol.51 , pp. 3661-3680
    • Congreve, M.1    Chessari, G.2    Tisi, D.3    Woodhead, A.J.4
  • 21
    • 0029836953 scopus 로고    scopus 로고
    • Discovering High-Affinity Ligands for Proteins: SAR by NMR
    • Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Discovering High-Affinity Ligands for Proteins: SAR by NMR Science 1996, 274, 1531-1534 10.1126/science.274.5292.1531
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 22
    • 2542643984 scopus 로고    scopus 로고
    • Integrating Fragment Assembly and Biophysical Methods in the Chemical Advancement of Small-Molecule Antagonists of IL-2: An Approach for Inhibiting Protein-Protein Interactions
    • Raimundo, B. C.; Oslob, J. D.; Braisted, A. C.; Hyde, J.; McDowell, R. S.; Randal, M.; Waal, N. D.; Wilkinson, J.; Yu, C. H.; Arkin, M. R. Integrating Fragment Assembly and Biophysical Methods in the Chemical Advancement of Small-Molecule Antagonists of IL-2: An Approach for Inhibiting Protein-Protein Interactions J. Med. Chem. 2004, 47, 3111-3130 10.1021/jm049967u
    • (2004) J. Med. Chem. , vol.47 , pp. 3111-3130
    • Raimundo, B.C.1    Oslob, J.D.2    Braisted, A.C.3    Hyde, J.4    McDowell, R.S.5    Randal, M.6    Waal, N.D.7    Wilkinson, J.8    Yu, C.H.9    Arkin, M.R.10
  • 23
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for High-Hanging Fruit in Drug Discovery at Protein-Protein Interfaces
    • Wells, J. A.; McClendon, C. L. Reaching for High-Hanging Fruit in Drug Discovery at Protein-Protein Interfaces Nature 2007, 450, 1001-1009 10.1038/nature06526
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 24
    • 84857712365 scopus 로고    scopus 로고
    • Protein-protein Interaction Inhibitors Get into the Groove
    • Mullard, A. Protein-protein Interaction Inhibitors Get into the Groove Nat. Rev. Drug Discovery 2012, 11, 173-175 10.1038/nrd3680
    • (2012) Nat. Rev. Drug Discovery , vol.11 , pp. 173-175
    • Mullard, A.1
  • 25
    • 58849145512 scopus 로고    scopus 로고
    • Predicting Druggable Binding Sites at the Protein-Protein Interface
    • Fuller, J. C.; Burgoyne, N. J.; Jackson, R. M. Predicting Druggable Binding Sites at the Protein-Protein Interface Drug Discovery Today 2009, 14, 155-161 10.1016/j.drudis.2008.10.009
    • (2009) Drug Discovery Today , vol.14 , pp. 155-161
    • Fuller, J.C.1    Burgoyne, N.J.2    Jackson, R.M.3
  • 28
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of Hot Spots in Protein Interfaces
    • Bogan, A. A.; Thorn, K. S. Anatomy of Hot Spots in Protein Interfaces J. Mol. Biol. 1998, 280, 1-9 10.1006/jmbi.1998.1843
    • (1998) J. Mol. Biol. , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 29
    • 3242879771 scopus 로고    scopus 로고
    • Computational Alanine Scanning of Protein-Protein Interfaces
    • Kortemme, T.; Kim, D. E.; Baker, D. Computational Alanine Scanning of Protein-Protein Interfaces Sci. Signaling 2004, 2004, pl2 10.1126/stke.2192004pl2
    • (2004) Sci. Signaling , vol.2004 , pp. 2
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 30
    • 84864451527 scopus 로고    scopus 로고
    • PocketQuery: Protein-Protein Interaction Inhibitor Starting Points from Protein-Protein Interaction Structure
    • Koes, D. R.; Camacho, C. J. PocketQuery: Protein-Protein Interaction Inhibitor Starting Points from Protein-Protein Interaction Structure Nucleic Acids Res. 2012, 40, W387-W392 10.1093/nar/gks336
    • (2012) Nucleic Acids Res. , vol.40 , pp. 387-W392
    • Koes, D.R.1    Camacho, C.J.2
  • 31
    • 34548779127 scopus 로고    scopus 로고
    • Hot Spots - A Review of the Protein-Protein Interface Determinant Amino-Acid Residues
    • Moreira, I. S.; Fernandes, P. A.; Ramos, M. J. Hot Spots - a Review of the Protein-Protein Interface Determinant Amino-Acid Residues Proteins: Struct., Funct., Genet. 2007, 68, 803-812 10.1002/prot.21396
    • (2007) Proteins: Struct., Funct., Genet. , vol.68 , pp. 803-812
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 32
    • 84879020527 scopus 로고    scopus 로고
    • Plucking the High Hanging Fruit: A Systematic Approach for Targeting Protein-Protein Interactions
    • Raj, M.; Bullock, B. N.; Arora, P. S. Plucking the High Hanging Fruit: A Systematic Approach for Targeting Protein-Protein Interactions Bioorg. Med. Chem. 2013, 21, 4051-4057 10.1016/j.bmc.2012.11.023
    • (2013) Bioorg. Med. Chem. , vol.21 , pp. 4051-4057
    • Raj, M.1    Bullock, B.N.2    Arora, P.S.3
  • 33
    • 84939970800 scopus 로고    scopus 로고
    • Structure-Based Inhibition of Protein-Protein Interactions
    • Watkins, A. M.; Arora, P. S. Structure-Based Inhibition of Protein-Protein Interactions Eur. J. Med. Chem. 2015, 94, 480-488 10.1016/j.ejmech.2014.09.047
    • (2015) Eur. J. Med. Chem. , vol.94 , pp. 480-488
    • Watkins, A.M.1    Arora, P.S.2
  • 34
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed Atlas of Surface Topography of Proteins
    • Binkowski, T. A.; Naghibzadeh, S.; Liang, J. CASTp: Computed Atlas of Surface Topography of Proteins Nucleic Acids Res. 2003, 31, 3352-3355 10.1093/nar/gkg512
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3352-3355
    • Binkowski, T.A.1    Naghibzadeh, S.2    Liang, J.3
  • 35
    • 0029935202 scopus 로고    scopus 로고
    • The Automatic Search for Ligand Binding Sites in Proteins of Known Three-Dimensional Structure Using only Geometric Criteria
    • Peters, K. P.; Fauck, J.; Frömmel, C. The Automatic Search for Ligand Binding Sites in Proteins of Known Three-Dimensional Structure Using Only Geometric Criteria J. Mol. Biol. 1996, 256, 201-213 10.1006/jmbi.1996.0077
    • (1996) J. Mol. Biol. , vol.256 , pp. 201-213
    • Peters, K.P.1    Fauck, J.2    Frömmel, C.3
  • 36
    • 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 Bioinf. 2009, 10, 168 10.1186/1471-2105-10-168
    • (2009) BMC Bioinf. , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 37
    • 0028881975 scopus 로고
    • SURFNET: A Program for Visualizing Molecular Surfaces, Cavities, and Intermolecular Interactions
    • Laskowski, R. A. SURFNET: A Program for Visualizing Molecular Surfaces, Cavities, and Intermolecular Interactions J. Mol. Graphics 1995, 13, 323-330 10.1016/0263-7855(95)00073-9
    • (1995) J. Mol. Graphics , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 38
    • 0342424187 scopus 로고    scopus 로고
    • Fast Prediction and Visualization of Protein Binding Pockets with PASS
    • Brady, G. P., Jr. ; Stouten, P. F. Fast Prediction and Visualization of Protein Binding Pockets with PASS J. Comput.-Aided Mol. Des. 2000, 14, 383-401 10.1023/A:1008124202956
    • (2000) J. Comput.-Aided Mol. Des. , vol.14 , pp. 383-401
    • Brady, G.P.1    Stouten, P.F.2
  • 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 2010, 26, 46-52 10.1093/bioinformatics/btp599
    • (2010) Bioinformatics , vol.26 , pp. 46-52
    • Yu, J.1    Zhou, Y.2    Tanaka, I.3    Yao, M.4
  • 40
    • 67849097355 scopus 로고    scopus 로고
    • SITEHOUND-Web: A Server for Ligand Binding Site Identification in Protein Structures
    • Hernandez, M.; Ghersi, D.; Sanchez, R. SITEHOUND-Web: A Server for Ligand Binding Site Identification in Protein Structures Nucleic Acids Res. 2009, 37, W413-W416 10.1093/nar/gkp281
    • (2009) Nucleic Acids Res. , vol.37 , pp. 413-W416
    • Hernandez, M.1    Ghersi, D.2    Sanchez, R.3
  • 41
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An Energy-Based Method for the Prediction of Protein-Ligand Binding Sites
    • Laurie, A. T. R.; Jackson, R. M. Q-SiteFinder: An Energy-Based Method for the Prediction of Protein-Ligand Binding Sites Bioinformatics 2005, 21, 1908-1916 10.1093/bioinformatics/bti315
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 42
    • 65249117514 scopus 로고    scopus 로고
    • Identifying and Characterizing Binding Sites and Assessing Druggability
    • Halgren, T. A. Identifying and Characterizing Binding Sites and Assessing Druggability J. Chem. Inf. Model. 2009, 49, 377-389 10.1021/ci800324m
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 377-389
    • Halgren, T.A.1
  • 43
    • 21044444449 scopus 로고    scopus 로고
    • Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
    • An, J.; Totrov, M.; Abagyan, R. Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes Mol. Cell. Proteomics 2005, 4, 752-761 10.1074/mcp.M400159-MCP200
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 752-761
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 44
    • 0027053611 scopus 로고
    • POCKET: A Computer Graphics Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino Acids
    • Levitt, D. G.; Banaszak, L. J. POCKET: A Computer Graphics Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino Acids J. Mol. Graphics 1992, 10, 229-234 10.1016/0263-7855(92)80074-N
    • (1992) J. Mol. Graphics , vol.10 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 45
    • 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. Graphics Modell. 1997, 15, 359-363 10.1016/S1093-3263(98)00002-3
    • (1997) J. Mol. Graphics Modell. , vol.15 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 46
    • 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. 2006, 6, 19 10.1186/1472-6807-6-19
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 47
    • 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. 2007, 1, 7 10.1186/1752-153X-1-7
    • (2007) Chem. Cent. J. , vol.1 , pp. 7
    • Weisel, M.1    Proschak, E.2    Schneider, G.3
  • 49
    • 79751535059 scopus 로고    scopus 로고
    • POVME: An Algorithm for Measuring Binding-Pocket Volumes
    • Durrant, J. D.; De Oliveira, C. A. F.; McCammon, J. A. POVME: An Algorithm for Measuring Binding-Pocket Volumes J. Mol. Graphics Modell. 2011, 29, 773-776 10.1016/j.jmgm.2010.10.007
    • (2011) J. Mol. Graphics Modell. , vol.29 , pp. 773-776
    • Durrant, J.D.1    De Oliveira, C.A.F.2    McCammon, J.A.3
  • 50
    • 84856084072 scopus 로고    scopus 로고
    • FTSite: High Accuracy Detection of Ligand Binding Sites on Unbound Protein Structures
    • Ngan, C.-H.; Hall, D. R.; Zerbe, B.; Grove, L. E.; Kozakov, D.; Vajda, S. FTSite: High Accuracy Detection of Ligand Binding Sites on Unbound Protein Structures Bioinformatics 2012, 28, 286-287 10.1093/bioinformatics/btr651
    • (2012) Bioinformatics , vol.28 , pp. 286-287
    • Ngan, C.-H.1    Hall, D.R.2    Zerbe, B.3    Grove, L.E.4    Kozakov, D.5    Vajda, S.6
  • 51
    • 84901596602 scopus 로고    scopus 로고
    • Computational Method to Identify Druggable Binding Sites That Target Protein-Protein Interactions
    • Li, H.; Kasam, V.; Tautermann, C. S.; Seeliger, D.; Vaidehi, N. Computational Method to Identify Druggable Binding Sites That Target Protein-Protein Interactions J. Chem. Inf. Model. 2014, 54, 1391-1400 10.1021/ci400750x
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1391-1400
    • Li, H.1    Kasam, V.2    Tautermann, C.S.3    Seeliger, D.4    Vaidehi, N.5
  • 52
    • 23144462493 scopus 로고    scopus 로고
    • MEDock: A Web Server for Efficient Prediction of Ligand Binding Sites Based on a Novel Optimization Algorithm
    • Chang, D. T.-H.; Oyang, Y.-J.; Lin, J.-H. MEDock: A Web Server for Efficient Prediction of Ligand Binding Sites Based on a Novel Optimization Algorithm Nucleic Acids Res. 2005, 33, W233-W238 10.1093/nar/gki586
    • (2005) Nucleic Acids Res. , vol.33 , pp. 233-W238
    • Chang, D.T.-H.1    Oyang, Y.-J.2    Lin, J.-H.3
  • 53
    • 77956308900 scopus 로고    scopus 로고
    • Binding-Site Assessment by Virtual Fragment Screening
    • Huang, N.; Jacobson, M. P. Binding-Site Assessment by Virtual Fragment Screening PLoS One 2010, 5, e10109 10.1371/journal.pone.0010109
    • (2010) PLoS One , vol.5 , pp. 10109
    • Huang, N.1    Jacobson, M.P.2
  • 55
    • 33749506205 scopus 로고    scopus 로고
    • Methods for the Prediction of Protein-Ligand Binding Sites for Structure-Based Drug Design and Virtual Ligand Screening
    • Laurie, A. T. R.; Jackson, R. M. Methods for the Prediction of Protein-Ligand Binding Sites for Structure-Based Drug Design and Virtual Ligand Screening Curr. Protein Pept. Sci. 2006, 7, 395-406 10.2174/138920306778559386
    • (2006) Curr. Protein Pept. Sci. , vol.7 , pp. 395-406
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 56
    • 61449104961 scopus 로고    scopus 로고
    • Fragment-Based Identification of Druggable "hot Spots" of Proteins Using Fourier Domain Correlation Techniques
    • Brenke, R.; Kozakov, D.; Chuang, G.-Y.; Beglov, D.; Hall, D.; Landon, M. R.; Mattos, C.; Vajda, S. Fragment-Based Identification of Druggable "Hot Spots" of Proteins Using Fourier Domain Correlation Techniques Bioinformatics 2009, 25, 621-627 10.1093/bioinformatics/btp036
    • (2009) Bioinformatics , vol.25 , pp. 621-627
    • Brenke, R.1    Kozakov, D.2    Chuang, G.-Y.3    Beglov, D.4    Hall, D.5    Landon, M.R.6    Mattos, C.7    Vajda, S.8
  • 58
    • 84865494461 scopus 로고    scopus 로고
    • Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces
    • Zerbe, B. S.; Hall, D. R.; Vajda, S.; Whitty, A.; Kozakov, D. Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces J. Chem. Inf. Model. 2012, 52, 2236-2244 10.1021/ci300175u
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2236-2244
    • Zerbe, B.S.1    Hall, D.R.2    Vajda, S.3    Whitty, A.4    Kozakov, D.5
  • 59
    • 84858044079 scopus 로고    scopus 로고
    • Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery
    • Hall, D. R.; Ngan, C. H.; Zerbe, B. S.; Kozakov, D.; Vajda, S. Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery J. Chem. Inf. Model. 2012, 52, 199-209 10.1021/ci200468p
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 199-209
    • Hall, D.R.1    Ngan, C.H.2    Zerbe, B.S.3    Kozakov, D.4    Vajda, S.5
  • 60
    • 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. 2010, 50, 2041-2052 10.1021/ci100241y
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2041-2052
    • Volkamer, A.1    Griewel, A.2    Grombacher, T.3    Rarey, M.4
  • 61
    • 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. 2012, 52, 360-372 10.1021/ci200454v
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 360-372
    • Volkamer, A.1    Kuhn, D.2    Grombacher, T.3    Rippmann, F.4    Rarey, M.5
  • 62
    • 84940204987 scopus 로고    scopus 로고
    • Molecular Operating Environment (MOE), 2013.08; Chemical Computing Group, Inc.: Montreal, QC, Canada, 2014
    • Molecular Operating Environment (MOE), 2013.08; Chemical Computing Group, Inc.: Montreal, QC, Canada, 2014.
  • 64
    • 84922813362 scopus 로고    scopus 로고
    • Small-Molecule Inhibitors of the MDM2-p53 Protein-Protein Interaction (MDM2 Inhibitors) in Clinical Trials for Cancer Treatment
    • Zhao, Y.; Aguilar, A.; Bernard, D.; Wang, S. Small-Molecule Inhibitors of the MDM2-p53 Protein-Protein Interaction (MDM2 Inhibitors) in Clinical Trials for Cancer Treatment J. Med. Chem. 2015, 58, 1038-1052 10.1021/jm501092z
    • (2015) J. Med. Chem. , vol.58 , pp. 1038-1052
    • Zhao, Y.1    Aguilar, A.2    Bernard, D.3    Wang, S.4
  • 65
    • 0030614915 scopus 로고    scopus 로고
    • Structure of Bcl-xL-Bak Peptide Complex: Recognition between Regulators of Apoptosis
    • Sattler, M. Structure of Bcl-xL-Bak Peptide Complex: Recognition Between Regulators of Apoptosis Science (Washington, DC, U. S.) 1997, 275, 983-986 10.1126/science.275.5302.983
    • (1997) Science (Washington, DC, U. S.) , vol.275 , pp. 983-986
    • Sattler, M.1
  • 67
    • 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. 1998, 7, 1884-1897 10.1002/pro.5560070905
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 68
    • 77949743743 scopus 로고    scopus 로고
    • Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database
    • Bourgeas, R.; Basse, M.-J.; Morelli, X.; Roche, P. Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database PLoS One 2010, 5, e9598 10.1371/journal.pone.0009598
    • (2010) PLoS One , vol.5 , pp. 9598
    • Bourgeas, R.1    Basse, M.-J.2    Morelli, X.3    Roche, P.4
  • 69
    • 84876546810 scopus 로고    scopus 로고
    • 2P2Idb: A Structural Database Dedicated to Orthosteric Modulation of Protein-Protein Interactions
    • Basse, M. J.; Betzi, S.; Bourgeas, R.; Bouzidi, S.; Chetrit, B.; Hamon, V.; Morelli, X.; Roche, P. 2P2Idb: A Structural Database Dedicated to Orthosteric Modulation of Protein-Protein Interactions Nucleic Acids Res. 2013, 41, D824-D827 10.1093/nar/gks1002
    • (2013) Nucleic Acids Res. , vol.41 , pp. 824-D827
    • Basse, M.J.1    Betzi, S.2    Bourgeas, R.3    Bouzidi, S.4    Chetrit, B.5    Hamon, V.6    Morelli, X.7    Roche, P.8
  • 70
    • 1842850600 scopus 로고    scopus 로고
    • Voronoi and Voronoi-Related Tessellations in Studies of Protein Structure and Interaction
    • Poupon, A. Voronoi and Voronoi-Related Tessellations in Studies of Protein Structure and Interaction Curr. Opin. Struct. Biol. 2004, 14, 233-241 10.1016/j.sbi.2004.03.010
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 233-241
    • Poupon, A.1
  • 71
    • 0015977588 scopus 로고
    • The Interpretation of Protein Structures: Total Volume, Group Volume Distributions and Packing Density
    • Richards, F. M. The Interpretation of Protein Structures: Total Volume, Group Volume Distributions and Packing Density J. Mol. Biol. 1974, 82, 1-14 10.1016/0022-2836(74)90570-1
    • (1974) J. Mol. Biol. , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 76
    • 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. 2007, 50, 3457-3464 10.1021/jm070095g
    • (2007) J. Med. Chem. , vol.50 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 78
    • 77954260900 scopus 로고    scopus 로고
    • ANCHOR: A Web Server and Database for Analysis of Protein-Protein Interaction Binding Pockets for Drug Discovery
    • Meireles, L. M. C.; Dömling, A. S.; Camacho, C. J. ANCHOR: A Web Server and Database for Analysis of Protein-Protein Interaction Binding Pockets for Drug Discovery Nucleic Acids Res. 2010, 38, W407-W411 10.1093/nar/gkq502
    • (2010) Nucleic Acids Res. , vol.38 , pp. 407-W411
    • Meireles, L.M.C.1    Dömling, A.S.2    Camacho, C.J.3
  • 80
    • 84895779578 scopus 로고    scopus 로고
    • Drugging the p53 Pathway: Understanding the Route to Clinical Efficacy
    • Khoo, K. H.; Hoe, K. K.; Verma, C. S.; Lane, D. P. Drugging the p53 Pathway: Understanding the Route to Clinical Efficacy Nat. Rev. Drug Discovery 2014, 13, 217-236 10.1038/nrd4236
    • (2014) Nat. Rev. Drug Discovery , vol.13 , pp. 217-236
    • Khoo, K.H.1    Hoe, K.K.2    Verma, C.S.3    Lane, D.P.4
  • 81
    • 77951766329 scopus 로고    scopus 로고
    • Systematic Mutational Analysis of Peptide Inhibition of the p53-MDM2/MDMX Interactions
    • Li, C.; Pazgier, M.; Li, C.; Yuan, W.; Liu, M.; Wei, G.; Lu, W.-Y.; Lu, W. Systematic Mutational Analysis of Peptide Inhibition of the p53-MDM2/MDMX Interactions J. Mol. Biol. 2010, 398, 200-213 10.1016/j.jmb.2010.03.005
    • (2010) J. Mol. Biol. , vol.398 , pp. 200-213
    • Li, C.1    Pazgier, M.2    Li, C.3    Yuan, W.4    Liu, M.5    Wei, G.6    Lu, W.-Y.7    Lu, W.8
  • 83
    • 77952331776 scopus 로고    scopus 로고
    • A Left-Handed Solution to Peptide Inhibition of the p53-MDM2 Interaction
    • Liu, M.; Pazgier, M.; Li, C.; Yuan, W.; Li, C.; Lu, W. A Left-Handed Solution to Peptide Inhibition of the p53-MDM2 Interaction Angew. Chem., Int. Ed. 2010, 49, 3649-3652 10.1002/anie.201000329
    • (2010) Angew. Chem., Int. Ed. , vol.49 , pp. 3649-3652
    • Liu, M.1    Pazgier, M.2    Li, C.3    Yuan, W.4    Li, C.5    Lu, W.6
  • 85
    • 0030575937 scopus 로고    scopus 로고
    • Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain
    • Kussie, P. H.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, J.; Levine, A. J.; Pavletich, N. P. Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain Science 1996, 274, 948-953 10.1126/science.274.5289.948
    • (1996) Science , vol.274 , pp. 948-953
    • Kussie, P.H.1    Gorina, S.2    Marechal, V.3    Elenbaas, B.4    Moreau, J.5    Levine, A.J.6    Pavletich, N.P.7
  • 86
    • 20444463203 scopus 로고    scopus 로고
    • Structure of Free MDM2 N-Terminal Domain Reveals Conformational Adjustments That Accompany p53-Binding
    • Uhrinova, S.; Uhrin, D.; Powers, H.; Watt, K.; Zheleva, D.; Fischer, P.; McInnes, C.; Barlow, P. N. Structure of Free MDM2 N-Terminal Domain Reveals Conformational Adjustments That Accompany p53-Binding J. Mol. Biol. 2005, 350, 587-598 10.1016/j.jmb.2005.05.010
    • (2005) J. Mol. Biol. , vol.350 , pp. 587-598
    • Uhrinova, S.1    Uhrin, D.2    Powers, H.3    Watt, K.4    Zheleva, D.5    Fischer, P.6    McInnes, C.7    Barlow, P.N.8
  • 88
    • 84865494461 scopus 로고    scopus 로고
    • Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces
    • Zerbe, B. S.; Hall, D. R.; Vajda, S.; Whitty, A.; Kozakov, D. Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces J. Chem. Inf. Model. 2012, 52, 2236-2244 10.1021/ci300175u
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2236-2244
    • Zerbe, B.S.1    Hall, D.R.2    Vajda, S.3    Whitty, A.4    Kozakov, D.5
  • 89
    • 0016708122 scopus 로고
    • Principles of Protein-Protein Recognition
    • Chothia, C.; Janin, J. Principles of Protein-Protein Recognition Nature 1975, 256, 705-708 10.1038/256705a0
    • (1975) Nature , vol.256 , pp. 705-708
    • Chothia, C.1    Janin, J.2
  • 90
    • 84860838201 scopus 로고    scopus 로고
    • Structure-Based Computational Analysis of Protein Binding Sites for Function and Druggability Prediction
    • Nisius, B.; Sha, F.; Gohlke, H. Structure-Based Computational Analysis of Protein Binding Sites for Function and Druggability Prediction J. Biotechnol. 2012, 159, 123-134 10.1016/j.jbiotec.2011.12.005
    • (2012) J. Biotechnol. , vol.159 , pp. 123-134
    • Nisius, B.1    Sha, F.2    Gohlke, H.3
  • 91
    • 84872225092 scopus 로고    scopus 로고
    • On the Binding Affinity of Macromolecular Interactions: Daring to Ask Why Proteins Interact
    • Kastritis, P. L.; Bonvin, A. M. J. J. On the Binding Affinity of Macromolecular Interactions: Daring to Ask Why Proteins Interact J. R. Soc., Interface 2012, 10, 20120835 10.1098/rsif.2012.0835
    • (2012) J. R. Soc., Interface , vol.10 , pp. 20120835
    • Kastritis, P.L.1    Bonvin, A.M.J.J.2
  • 92
    • 84902438255 scopus 로고    scopus 로고
    • Improved Protein-Ligand Binding Affinity Prediction by Using a Curvature-Dependent Surface-Area Model
    • Cao, Y.; Li, L. Improved Protein-Ligand Binding Affinity Prediction by Using a Curvature-Dependent Surface-Area Model Bioinformatics 2014, 30, 1674-1680 10.1093/bioinformatics/btu104
    • (2014) Bioinformatics , vol.30 , pp. 1674-1680
    • Cao, Y.1    Li, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.