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Volumn 53, Issue 5, 2013, Pages 1235-1252

TRAPP: A tool for analysis of Transient binding Pockets in Proteins

Author keywords

[No Author keywords available]

Indexed keywords

MOTION TRACKING; TRANSIENT ANALYSIS;

EID: 84878181372     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4000294     Document Type: Article
Times cited : (63)

References (46)
  • 1
    • 76649139794 scopus 로고    scopus 로고
    • Computational approaches to identifying and characterizing protein binding sites for ligand design
    • Henrich, S.; Salo-Ahen, O. M.; Huang, B.; Rippmann, F. F.; Cruciani, G.; Wade, R. C. Computational approaches to identifying and characterizing protein binding sites for ligand design J. Mol. Recognit. 2010, 23, 209-219
    • (2010) J. Mol. Recognit. , vol.23 , pp. 209-219
    • Henrich, S.1    Salo-Ahen, O.M.2    Huang, B.3    Rippmann, F.F.4    Cruciani, G.5    Wade, R.C.6
  • 2
    • 33749506205 scopus 로고    scopus 로고
    • Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
    • DOI 10.2174/138920306778559386
    • Laurie, T. R. A.; Jackson, R. M. Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual screening Curr. Protein Peptide Sci. 2006, 7, 395-406 (Pubitemid 44524489)
    • (2006) Current Protein and Peptide Science , vol.7 , Issue.5 , pp. 395-406
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 5
    • 80054807339 scopus 로고    scopus 로고
    • Receptor flexibility in small-molecule docking calculations
    • Kokh, D. B.; Wade, R. C.; Wenzel, W. Receptor flexibility in small-molecule docking calculations WIREs Comput. Mol. Sci. 2011, 1, 298-314
    • (2011) WIREs Comput. Mol. Sci. , vol.1 , pp. 298-314
    • Kokh, D.B.1    Wade, R.C.2    Wenzel, W.3
  • 6
    • 84861118556 scopus 로고    scopus 로고
    • Outstanding challenges in protein-ligand docking and structure-based virtual screening
    • Waszkowycz, B.; Clark, D. E.; Gancia, E. Outstanding challenges in protein-ligand docking and structure-based virtual screening WIREs Comp. Mol. Sci. 2011, 1, 229-259
    • (2011) WIREs Comp. Mol. Sci. , vol.1 , pp. 229-259
    • Waszkowycz, B.1    Clark, D.E.2    Gancia, E.3
  • 7
    • 33746076877 scopus 로고    scopus 로고
    • Effects of conformational dynamics on predicted protein druggability
    • DOI 10.1002/cmdc.200500013
    • Brown, S. P.; Hajduk, P. J. Effects of conformational dynamics on predicted protein druggability ChemMedChem 2006, 1, 70-72 (Pubitemid 44104979)
    • (2006) ChemMedChem , vol.1 , Issue.1 , pp. 70-72
    • Brown, S.P.1    Hajduk, P.J.2
  • 8
    • 33751423377 scopus 로고    scopus 로고
    • How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding
    • DOI 10.1016/j.jmb.2006.09.062, PII S0022283606012861
    • Gunasekaran, K.; Nussinov, R. How different are structurally flexible and rigid regions? Sequence and structural features discriminating proteins that do and do not undergo conformational changes upon ligand binding J. Mol. Biol. 2007, 365, 257-273 (Pubitemid 44821204)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.1 , pp. 257-273
    • Gunasekaran, K.1    Nussinov, R.2
  • 9
    • 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
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative Curr. Opin. Struct. Biol. 2008, 18, 178-184
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 11
    • 79958164854 scopus 로고    scopus 로고
    • A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks
    • Stein, A.; Rueda, M.; Panjkovich, A.; Orozco, M.; Aloy, P. A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks Structure 2011, 19, 881-889
    • (2011) Structure , vol.19 , pp. 881-889
    • Stein, A.1    Rueda, M.2    Panjkovich, A.3    Orozco, M.4    Aloy, P.5
  • 12
    • 0033135477 scopus 로고    scopus 로고
    • Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
    • DOI 10.1002/(SICI)1097-0134(19990501)35:2<153::AID-PROT2>3.0.CO;2-E
    • Mangoni, M.; Roccatano, D.; Di Nola, A. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation Proteins 1999, 35, 153-162 (Pubitemid 29165129)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.2 , pp. 153-162
    • Mangoni, M.1    Roccatano, D.2    Di Nola, A.3
  • 13
    • 34547583152 scopus 로고    scopus 로고
    • Transient pockets on protein surfaces involved in protein-protein interaction
    • DOI 10.1021/jm070095g
    • Eyrisch, S.; Helms, V. Transient pockets on protein surfaces involved in protein-protein interactions J. Med. Chem. 2007, 50, 3457-3464 (Pubitemid 47195455)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.15 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 15
    • 84878189196 scopus 로고    scopus 로고
    • How transient pockets open on the surface of the MDM2 protein
    • Eyrisch, S.; Helms, V. How transient pockets open on the surface of the MDM2 protein Chem. Central J. 2008, 2 (Suppl I) P34
    • (2008) Chem. Central J. , vol.2 , Issue.SUPPL. I , pp. 34
    • Eyrisch, S.1    Helms, V.2
  • 16
  • 17
    • 82255164267 scopus 로고    scopus 로고
    • MDpocket: Open source cavity detection and characterization on molecular dynamics trajectories
    • Schmidtke, P.; Bidon-Chanal, A.; Luque, F. J.; Barril, X. MDpocket: open source cavity detection and characterization on molecular dynamics trajectories Bioinformatics 2011, 27, 3276-3285
    • (2011) Bioinformatics , vol.27 , pp. 3276-3285
    • Schmidtke, P.1    Bidon-Chanal, A.2    Luque, F.J.3    Barril, X.4
  • 18
    • 79959758718 scopus 로고    scopus 로고
    • Predictive power of molecular dynamics receptor structures in virtual screening
    • Nichols, S. E.; Baron, R.; Ivetac, A.; MaCammon, J. A. Predictive power of molecular dynamics receptor structures in virtual screening J. Chem. Inf. Model. 2011, 51, 1439-1446
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1439-1446
    • Nichols, S.E.1    Baron, R.2    Ivetac, A.3    MacAmmon, J.A.4
  • 19
    • 35748982413 scopus 로고    scopus 로고
    • Geometry-Based Sampling of Conformational Transitions in Proteins
    • DOI 10.1016/j.str.2007.09.017, PII S0969212607003681
    • Seeliger, D.; Haas, J.; de Groot, B. Geometry-based Sampling of conformational transitions in protiens Structure 2007, 15, 1482-1492 (Pubitemid 350051928)
    • (2007) Structure , vol.15 , Issue.11 , pp. 1482-1492
    • Seeliger, D.1    Haas, J.2    De Groot, B.L.3
  • 20
    • 58149333699 scopus 로고    scopus 로고
    • What induces pocket openings on protein surface patches involved in protein-protein interactions?
    • Eyrisch, S.; Helms, V. What induces pocket openings on protein surface patches involved in protein-protein interactions? J Comput.-Aided Mol. Des. 2009, 23, 73-86
    • (2009) J Comput.-Aided Mol. Des. , vol.23 , pp. 73-86
    • Eyrisch, S.1    Helms, V.2
  • 21
    • 76749123486 scopus 로고    scopus 로고
    • Conformational transitions upon ligand binding: Holo-structure prediction from apo-conformations
    • Seeliger, D.; de Groot, B. Conformational transitions upon ligand binding: holo-structure prediction from apo-conformations PLoS Comput. Biol. 2010, 6, e1000634-e1000641
    • (2010) PLoS Comput. Biol. , vol.6
    • Seeliger, D.1    De Groot, B.2
  • 22
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • DOI 10.1021/ja042260c
    • Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 2005, 127, 9632-9640 (Pubitemid 40934775)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.26 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 23
    • 84859166785 scopus 로고    scopus 로고
    • On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking
    • Dietzen, M.; Zotenko, E.; Hildebrandt, A.; Lengauer, T. On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking J. Chem. Inf. Mod. 2012, 52, 844-856
    • (2012) J. Chem. Inf. Mod. , vol.52 , pp. 844-856
    • Dietzen, M.1    Zotenko, E.2    Hildebrandt, A.3    Lengauer, T.4
  • 24
    • 84863393146 scopus 로고    scopus 로고
    • Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets
    • Ashford, P.; Moss, D. S.; Alex, A.; Yeap, S. K.; Povia, A.; Nobeli, I.; Williams, M. A. Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets BMC Bioinf. 2012, 13, 1471
    • (2012) BMC Bioinf. , vol.13 , pp. 1471
    • Ashford, P.1    Moss, D.S.2    Alex, A.3    Yeap, S.K.4    Povia, A.5    Nobeli, I.6    Williams, M.A.7
  • 25
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • DOI 10.1016/S1093-3263(98)00002-3, PII S1093326398000023
    • Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: Automatic and efficient method detection of potential small molecule-binding sites in proteins J. Mol. Graphics. Modell. 1997, 15, 359-363 (Pubitemid 28409807)
    • (1997) Journal of Molecular Graphics and Modelling , vol.15 , Issue.6 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 26
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • DOI 10.1023/A:1008124202956
    • Brady, G. P.; Stouten, P. Fast prediction and visualization of protein binding pockets with PASS J Comput.-Aided Drug. Des. 2000, 14, 383-401 (Pubitemid 30219399)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.4 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.W.2
  • 27
    • 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, 168-179
    • (2009) BMC Bioinf. , vol.10 , pp. 168-179
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 28
    • 77950423796 scopus 로고    scopus 로고
    • A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: Application to ligand prediction
    • Hoffmann, B.; Zaslavskiy, M.; Vert, J.-P.; Stoven, V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction BMC Bioinf. 2010, 11, 99-115
    • (2010) BMC Bioinf. , vol.11 , pp. 99-115
    • Hoffmann, B.1    Zaslavskiy, M.2    Vert, J.-P.3    Stoven, V.4
  • 29
    • 79955574923 scopus 로고    scopus 로고
    • version 1.4.1; Schrödinger, LLC, New York; (accessed January).
    • The PyMOL Molecular Graphics System, version 1.4.1; Schrödinger, LLC, New York; http://www.pymol.org (accessed January 2012).
    • (2012) The PyMOL Molecular Graphics System
  • 30
    • 84878195471 scopus 로고    scopus 로고
    • Jmol: an open-source Java viewer for chemical structures in 3D. (accessed Jan).
    • Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ (accessed Jan 2012).
    • (2012)
  • 32
    • 84878204757 scopus 로고    scopus 로고
    • SciPy: Open Source Scientific Tools for Python. (accessed Apr.1)
    • Jones, E.; Oliphant, T.; Peterson, P. SciPy: Open Source Scientific Tools for Python. http://www.scipy.org (accessed Apr.1, 2012)
    • (2012)
    • Jones, E.1    Oliphant, T.2    Peterson, P.3
  • 38
    • 84857291408 scopus 로고    scopus 로고
    • Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface
    • Metz, A.; Pfleger, C.; Kopitz, H.; Pfeiffer-Marek, S.; Baringhaus, K. H.; Gohlke, H. Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface J. Chem. Inf. Mod. 2012, 52, 120-133
    • (2012) J. Chem. Inf. Mod. , vol.52 , pp. 120-133
    • Metz, A.1    Pfleger, C.2    Kopitz, H.3    Pfeiffer-Marek, S.4    Baringhaus, K.H.5    Gohlke, H.6
  • 39
    • 84878185727 scopus 로고    scopus 로고
    • version 9.2; Schrödinger, LLC, New York.
    • Maestro, version 9.2; Schrödinger, LLC, New York, 2011; http://www.schrodinger.com/.
    • (2011) Maestro
  • 40
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 41
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • DOI 10.1021/ja9621760, PII S0002786396021762
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 (Pubitemid 26399746)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 42
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
    • (2004) J. Comput. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 44
    • 33745880692 scopus 로고    scopus 로고
    • Computational Sampling of a Cryptic Drug Binding Site in a Protein Receptor: Explicit Solvent Molecular Dynamics and Inhibitor Docking to p38 MAP Kinase
    • DOI 10.1016/j.jmb.2006.03.021, PII S002228360600341X
    • Frembgen-Kesner, T.; Elcock, A. H. Computational Sampling of a Cryptic Drug Binding Site in a Protein Receptor: Explicit Solvent Molecular Dynamics and Inhibitor Docking to p38 MAP Kinase J. Mol. Biol. 2006, 359, 202-214 (Pubitemid 44287824)
    • (2006) Journal of Molecular Biology , vol.359 , Issue.1 , pp. 202-214
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 46
    • 65349192770 scopus 로고    scopus 로고
    • Probing the flexibility of large conformational changes in protein structures through local perturbations
    • Ho, B. K.; Agard, D. A. Probing the flexibility of large conformational changes in protein structures through local perturbations PLoS Comput. Biol. 2009, 5, e1000343-e1000313
    • (2009) PLoS Comput. Biol. , vol.5
    • Ho, B.K.1    Agard, D.A.2


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