메뉴 건너뛰기




Volumn 55, Issue 4, 2015, Pages 882-895

PockDrug: A model for predicting pocket druggability that overcomes pocket estimation uncertainties

Author keywords

[No Author keywords available]

Indexed keywords

DISCRIMINANT ANALYSIS;

EID: 84928681155     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci5006004     Document Type: Article
Times cited : (79)

References (43)
  • 2
    • 84907463401 scopus 로고    scopus 로고
    • Design, Synthesis, and Structure - Activity and Structure - Pharmacokinetic Relationship Studies of Novel [6,6,5] Tricyclic Fused Oxazolidinones Leading to the Discovery of a Potent, Selective, and Orally Bioavailable FXa Inhibitor
    • Xue, T.; Ding, S.; Guo, B.; Zhou, Y.; Sun, P.; Wang, H.; Chu, W.; Gong, G.; Wang, Y.; Chen, X.; Yang, Y. Design, Synthesis, and Structure-Activity and Structure-Pharmacokinetic Relationship Studies of Novel [6,6,5] Tricyclic Fused Oxazolidinones Leading to the Discovery of a Potent, Selective, and Orally Bioavailable FXa Inhibitor J. Med. Chem. 2014, 57, 7770-7791
    • (2014) J. Med. Chem. , vol.57 , pp. 7770-7791
    • Xue, T.1    Ding, S.2    Guo, B.3    Zhou, Y.4    Sun, P.5    Wang, H.6    Chu, W.7    Gong, G.8    Wang, Y.9    Chen, X.10    Yang, Y.11
  • 4
    • 17144373303 scopus 로고    scopus 로고
    • Druggability Indices for Protein Targets Derived from NMR-Based Screening Data
    • Hajduk, P. J.; Huth, J. R.; Fesik, S. W. Druggability Indices for Protein Targets Derived from NMR-Based Screening Data J. Med. Chem. 2005, 48, 2518-2525
    • (2005) J. Med. Chem. , vol.48 , pp. 2518-2525
    • Hajduk, P.J.1    Huth, J.R.2    Fesik, S.W.3
  • 6
    • 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 Discovery Today 2003, 8, 1067-1077
    • (2003) Drug Discovery Today , vol.8 , pp. 1067-1077
    • Brown, D.1    Superti-Furga, G.2
  • 7
    • 54849423239 scopus 로고    scopus 로고
    • Predicting Selectivity and Druggability in Drug Discovery
    • Cheng, A. C. Predicting Selectivity and Druggability in Drug Discovery Annu. Rep. Comput. Chem. 2008, 4, 23-37
    • (2008) Annu. Rep. Comput. Chem. , vol.4 , pp. 23-37
    • Cheng, A.C.1
  • 8
    • 79960985571 scopus 로고    scopus 로고
    • Structure-Based Druggability Assessment - Identifying Suitable Targets for Small Molecule Therapeutics
    • Fauman, E. B.; Rai, B. K.; Huang, E. S. Structure-Based Druggability Assessment - Identifying Suitable Targets for Small Molecule Therapeutics Curr. Opin. Chem. Biol. 2011, 15, 463-468
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 463-468
    • Fauman, E.B.1    Rai, B.K.2    Huang, E.S.3
  • 10
    • 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
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 377-389
    • Halgren, T.A.1
  • 11
    • 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. 2012, 52, 2287-2299
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2287-2299
    • Desaphy, J.1    Azdimousa, K.2    Kellenberger, E.3    Rognan, D.4
  • 12
    • 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. 2010, 53, 5858-5867
    • (2010) J. Med. Chem. , vol.53 , pp. 5858-5867
    • Schmidtke, P.1    Barril, X.2
  • 13
    • 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. 2012, 52, 1027-1038
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 1027-1038
    • Perola, E.1    Herman, L.2    Weiss, J.3
  • 14
    • 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.; Sarkar, A.; Schmitt, S.; Brenk, R. DrugPred: A Structure-Based Approach to Predict Protein Druggability Developed Using an Extensive Nonredundant Data Set J. Chem. Inf. Model. 2011, 51, 2829-2842
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2829-2842
    • Krasowski, A.1    Muthas, D.2    Sarkar, A.3    Schmitt, S.4    Brenk, R.5
  • 15
    • 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
    • (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
  • 16
    • 77955517509 scopus 로고    scopus 로고
    • Druggable Pockets and Binding Site Centric Chemical Space: A Paradigm Shift in Drug Discovery
    • Pérot, S.; Sperandio, O.; Miteva, M. a; Camproux, A.-C.; Villoutreix, B. O. Druggable Pockets and Binding Site Centric Chemical Space: A Paradigm Shift in Drug Discovery Drug Discovery Today 2010, 15, 656-667
    • (2010) Drug Discovery Today , vol.15 , pp. 656-667
    • Pérot, S.1    Sperandio, O.2    Miteva, M.A.3    Camproux, A.-C.4    Villoutreix, B.O.5
  • 17
    • 84887265599 scopus 로고    scopus 로고
    • A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
    • Gao, M.; Skolnick, J. A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins PLoS Comput. Biol. 2013, 9, e1003302
    • (2013) PLoS Comput. Biol. , vol.9
    • Gao, M.1    Skolnick, J.2
  • 18
    • 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) 389
    • (1997) J. Mol. Graphics Modell. , vol.15 , Issue.359-363 , pp. 389
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 19
    • 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
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2041-2052
    • Volkamer, A.1    Griewel, A.2    Grombacher, T.3    Rarey, M.4
  • 20
    • 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 2009, 10, 168
    • (2009) BMC Bioinformatics , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 21
    • 44349119204 scopus 로고    scopus 로고
    • A Simple and Fuzzy Method to Align and Compare Druggable Ligand-Binding Sites
    • Schalon, C.; Surgand, J.-S.; Kellenberger, E.; Rognan, D. A Simple and Fuzzy Method to Align and Compare Druggable Ligand-Binding Sites Proteins 2008, 71, 1755-1778
    • (2008) Proteins , vol.71 , pp. 1755-1778
    • Schalon, C.1    Surgand, J.-S.2    Kellenberger, E.3    Rognan, D.4
  • 22
    • 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. 2010, 50, 123-135
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 123-135
    • Weill, N.1    Rognan, D.2
  • 23
    • 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 2008, 9, 543
    • (2008) BMC Bioinformatics , vol.9 , pp. 543
    • Yeturu, K.1    Chandra, N.2
  • 24
    • 77956040809 scopus 로고    scopus 로고
    • Pocket Similarity: Are Alpha Carbons Enough?
    • Feldman, H. J.; Labute, P. Pocket Similarity: Are Alpha Carbons Enough? J. Chem. Inf. Model. 2010, 50, 1466-1475
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1466-1475
    • Feldman, H.J.1    Labute, P.2
  • 25
    • 84901317146 scopus 로고    scopus 로고
    • Knowledge-Based Fragment Binding Prediction
    • Tang, G. W.; Altman, R. B. Knowledge-Based Fragment Binding Prediction PLoS Comput. Biol. 2014, 10, e1003589
    • (2014) PLoS Comput. Biol. , vol.10
    • Tang, G.W.1    Altman, R.B.2
  • 26
    • 84888182124 scopus 로고    scopus 로고
    • A Molecular Pathway for the Egress of Ammonia Produced by Nitrogenase
    • Dance, I. A Molecular Pathway for the Egress of Ammonia Produced by Nitrogenase Sci. Rep. 2013, 3, 3237
    • (2013) Sci. Rep. , vol.3 , pp. 3237
    • Dance, I.1
  • 28
    • 84908114976 scopus 로고    scopus 로고
    • Tertiary Structure Prediction and Identification of Druggable Pocket in the Cancer Biomarker - Osteopontin-C
    • Sivakumar, S.; Niranjali Devaraj, S. Tertiary Structure Prediction and Identification of Druggable Pocket in the Cancer Biomarker-Osteopontin-C J. Diabetes Metab. Disord. 2014, 13, 13
    • (2014) J. Diabetes Metab. Disord. , vol.13 , pp. 13
    • Sivakumar, S.1    Niranjali Devaraj, S.2
  • 29
    • 17644392830 scopus 로고    scopus 로고
    • TM-Align: A Protein Structure Alignment Algorithm Based on the TM-Score
    • Zhang, Y.; Skolnick, J. TM-Align: A Protein Structure Alignment Algorithm Based on the TM-Score Nucleic Acids Res. 2005, 33, 2302-2309
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 31
    • 84928672137 scopus 로고    scopus 로고
    • version 4.0
    • Petitjean, M. RADI, version 4.0, 2014. http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.
    • (2014) RADI
    • Petitjean, M.1
  • 32
    • 77956040404 scopus 로고    scopus 로고
    • Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe
    • Milletti, F.; Vulpetti, A. Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe J. Chem. Inf. Model. 2010, 50, 1418-1431
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1418-1431
    • Milletti, F.1    Vulpetti, A.2
  • 33
    • 33745597909 scopus 로고    scopus 로고
    • Predicting Protein Interaction Sites: Binding Hot-Spots in Protein-Protein and Protein-Ligand Interfaces
    • Burgoyne, N. J.; Jackson, R. M. Predicting Protein Interaction Sites: Binding Hot-Spots in Protein-Protein and Protein-Ligand Interfaces Bioinformatics 2006, 22, 1335-1342
    • (2006) Bioinformatics , vol.22 , pp. 1335-1342
    • Burgoyne, N.J.1    Jackson, R.M.2
  • 34
    • 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
    • (2007) J. Med. Chem. , vol.50 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 35
    • 0020475449 scopus 로고
    • A Simple Method for Displaying the Hydropathic Character of a Protein
    • Kyte, J.; Doolittle, R. F. A Simple Method for Displaying the Hydropathic Character of a Protein J. Mol. Biol. 1982, 157, 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 36
    • 0000764772 scopus 로고
    • The Use of Multiple Measurements in Taxonomic Problems
    • Fisher, R. The Use of Multiple Measurements in Taxonomic Problems Ann. Eugen. 1936, 7, 179-188
    • (1936) Ann. Eugen. , vol.7 , pp. 179-188
    • Fisher, R.1
  • 37
    • 84912569628 scopus 로고    scopus 로고
    • Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple due to Inherent Shape Similarity
    • Krotzky, T.; Rickmeyer, T. Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple due to Inherent Shape Similarity J. Chem. Inf. Model. 2014, 54, 3229-3237
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 3229-3237
    • Krotzky, T.1    Rickmeyer, T.2
  • 38
    • 84874754249 scopus 로고    scopus 로고
    • APoc: Large-Scale Identification of Similar Protein Pockets
    • Gao, M.; Skolnick, J. APoc: Large-Scale Identification of Similar Protein Pockets Bioinformatics 2013, 29, 597-604
    • (2013) Bioinformatics , vol.29 , pp. 597-604
    • Gao, M.1    Skolnick, J.2
  • 39
    • 84924426339 scopus 로고    scopus 로고
    • A Collective Variable for the Rapid Exploration of Protein Druggability
    • Cuchillo, R.; Pinto-gil, K.; Michel, J. A Collective Variable for the Rapid Exploration of Protein Druggability J. Chem. Theory Comput. 2015, 11, 1292-1307
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 1292-1307
    • Cuchillo, R.1    Pinto-Gil, K.2    Michel, J.3
  • 40
    • 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. 2011, 159, 123-134
    • (2011) J. Biotechnol. , vol.159 , pp. 123-134
    • Nisius, B.1    Sha, F.2    Gohlke, H.3
  • 41
    • 0028301575 scopus 로고
    • Amino Acid Preferences at Protein Binding Sites
    • Villar, H. O.; Kauvar, L. M. Amino Acid Preferences at Protein Binding Sites FEBS Lett. 1994, 349, 125-130
    • (1994) FEBS Lett. , vol.349 , pp. 125-130
    • Villar, H.O.1    Kauvar, L.M.2
  • 43
    • 0000697995 scopus 로고
    • Applications of the Radius-Diameter Diagram to the Classification of Topological and Geometrical Shapes of Chemical Compounds
    • Petitjean, M. Applications of the Radius-Diameter Diagram to the Classification of Topological and Geometrical Shapes of Chemical Compounds J. Chem. Inf. Comput. Sci. 1992, 32, 331-337
    • (1992) J. Chem. Inf. Comput. Sci. , vol.32 , pp. 331-337
    • Petitjean, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.