메뉴 건너뛰기




Volumn 59, Issue 14, 2016, Pages 6891-6902

Protein-ligand informatics force field (PLIff): Toward a fully knowledge driven "force field" for biomolecular interactions

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 84979902232     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/acs.jmedchem.6b00716     Document Type: Article
Times cited : (20)

References (49)
  • 1
    • 14844284587 scopus 로고    scopus 로고
    • Application of Molecular Dynamics Simulations to Spin-Labeled Oligonucleotides
    • Darian, E.; Gannett, P. M. Application of Molecular Dynamics Simulations to Spin-Labeled Oligonucleotides J. Biomol. Struct. Dyn. 2005, 22, 579-593 10.1080/07391102.2005.10507028
    • (2005) J. Biomol. Struct. Dyn. , vol.22 , pp. 579-593
    • Darian, E.1    Gannett, P.M.2
  • 2
    • 33645941402 scopus 로고
    • The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin
    • Jorgensen, W. L.; Tirado-Rives, J. The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110, 1657-1666 10.1021/ja00214a001
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 3
    • 0028454828 scopus 로고
    • The Development of a Simple Empirical Scoring Function to Estimate the Binding Constant for a Protein-Ligand Complex of Known Three-Dimensional Structure
    • Bohm, H. J. The Development of a Simple Empirical Scoring Function to Estimate the Binding Constant for a Protein-Ligand Complex of Known Three-Dimensional Structure J. Comput.-Aided Mol. Des. 1994, 8, 243-256 10.1007/BF00126743
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 4
    • 0031226772 scopus 로고    scopus 로고
    • Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes J. Comput.-Aided Mol. Des. 1997, 11, 425-445 10.1023/A:1007996124545
    • (1997) J. Comput.-Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 7
    • 0035823226 scopus 로고    scopus 로고
    • SuperStar: Comparison of CSD and PDB-Based Interaction Fields as a Basis for the Prediction of Protein-Ligand Interactions1
    • Boer, D. R.; Kroon, J.; Cole, J. C.; Smith, B.; Verdonk, M. L. SuperStar: Comparison of CSD and PDB-Based Interaction Fields as a Basis for the Prediction of Protein-Ligand Interactions1 J. Mol. Biol. 2001, 312, 275-287 10.1006/jmbi.2001.4901
    • (2001) J. Mol. Biol. , vol.312 , pp. 275-287
    • Boer, D.R.1    Kroon, J.2    Cole, J.C.3    Smith, B.4    Verdonk, M.L.5
  • 8
    • 0033545622 scopus 로고    scopus 로고
    • A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach
    • Muegge, I.; Martin, Y. C. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach J. Med. Chem. 1999, 42, 791-804 10.1021/jm980536j
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 9
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-Based Scoring Function to Predict Protein-Ligand Interactions
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-Based Scoring Function to Predict Protein-Ligand Interactions J. Mol. Biol. 2000, 295, 337-356 10.1006/jmbi.1999.3371
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 10
    • 26444468103 scopus 로고    scopus 로고
    • General and Targeted Statistical Potentials for Protein-Ligand Interactions
    • Mooij, W. T.; Verdonk, M. L. General and Targeted Statistical Potentials for Protein-Ligand Interactions Proteins: Struct., Funct., Genet. 2005, 61, 272-287 10.1002/prot.20588
    • (2005) Proteins: Struct., Funct., Genet. , vol.61 , pp. 272-287
    • Mooij, W.T.1    Verdonk, M.L.2
  • 11
    • 80054943835 scopus 로고    scopus 로고
    • Dsx: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes
    • Neudert, G.; Klebe, G. Dsx: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes J. Chem. Inf. Model. 2011, 51, 2731-2745 10.1021/ci200274q
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2731-2745
    • Neudert, G.1    Klebe, G.2
  • 12
    • 0036773411 scopus 로고    scopus 로고
    • Quantification of Protein Surfaces, Volumes and Atom-Atom Contacts Using a Constrained Voronoi Procedure
    • McConkey, B. J.; Sobolev, V.; Edelman, M. Quantification of Protein Surfaces, Volumes and Atom-Atom Contacts Using a Constrained Voronoi Procedure Bioinformatics 2002, 18, 1365-1373 10.1093/bioinformatics/18.10.1365
    • (2002) Bioinformatics , vol.18 , pp. 1365-1373
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 13
    • 0037452894 scopus 로고    scopus 로고
    • Discrimination of Native Protein Structures Using Atom-Atom Contact Scoring
    • McConkey, B. J.; Sobolev, V.; Edelman, M. Discrimination of Native Protein Structures Using Atom-Atom Contact Scoring Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 3215-3220 10.1073/pnas.0535768100
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 3215-3220
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 14
    • 12044255753 scopus 로고
    • Scales of Solute Hydrogen-Bonding: Their Construction and Application to Physicochemical and Biochemical Processes
    • Abraham, M. H. Scales of Solute Hydrogen-Bonding: Their Construction and Application to Physicochemical and Biochemical Processes Chem. Soc. Rev. 1993, 22, 73-83 10.1039/cs9932200073
    • (1993) Chem. Soc. Rev. , vol.22 , pp. 73-83
    • Abraham, M.H.1
  • 15
    • 66149148957 scopus 로고    scopus 로고
    • Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Organic Compounds by Local Molecular Parameters
    • Schwobel, J.; Ebert, R. U.; Kuhne, R.; Schuurmann, G. Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Organic Compounds by Local Molecular Parameters J. Chem. Inf. Model. 2009, 49, 956-962 10.1021/ci900040z
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 956-962
    • Schwobel, J.1    Ebert, R.U.2    Kuhne, R.3    Schuurmann, G.4
  • 16
    • 84874046410 scopus 로고    scopus 로고
    • Halogen Bonding (X-Bonding): A Biological Perspective
    • Scholfield, M. R.; Zanden, C. M.; Carter, M.; Ho, P. S. Halogen Bonding (X-Bonding): A Biological Perspective Protein Sci. 2013, 22, 139-152 10.1002/pro.2201
    • (2013) Protein Sci. , vol.22 , pp. 139-152
    • Scholfield, M.R.1    Zanden, C.M.2    Carter, M.3    Ho, P.S.4
  • 18
    • 0030567353 scopus 로고    scopus 로고
    • The Nature and Geometry of Intermolecular Interactions between Halogens and Oxygen or Nitrogen
    • Lommerse, J. P. M.; Stone, A. J.; Taylor, R.; Allen, F. H. The Nature and Geometry of Intermolecular Interactions between Halogens and Oxygen or Nitrogen J. Am. Chem. Soc. 1996, 118, 3108-3116 10.1021/ja953281x
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3108-3116
    • Lommerse, J.P.M.1    Stone, A.J.2    Taylor, R.3    Allen, F.H.4
  • 19
    • 79959739959 scopus 로고    scopus 로고
    • Molecular Mechanical Study of Halogen Bonding in Drug Discovery
    • Ibrahim, M. A. Molecular Mechanical Study of Halogen Bonding in Drug Discovery J. Comput. Chem. 2011, 32, 2564-2574 10.1002/jcc.21836
    • (2011) J. Comput. Chem. , vol.32 , pp. 2564-2574
    • Ibrahim, M.A.1
  • 20
    • 84866682261 scopus 로고    scopus 로고
    • Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents
    • Jorgensen, W. L.; Schyman, P. Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents J. Chem. Theory Comput. 2012, 8, 3895-3801 10.1021/ct300180w
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 3801-3895
    • Jorgensen, W.L.1    Schyman, P.2
  • 21
    • 0028695270 scopus 로고
    • Extended Electron Distributions Applied to the Molecular Mechanics of Some Intermolecular Interactions
    • Vinter, J. G. Extended Electron Distributions Applied to the Molecular Mechanics of Some Intermolecular Interactions J. Comput.-Aided Mol. Des. 1994, 8, 653-668 10.1007/BF00124013
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 653-668
    • Vinter, J.G.1
  • 22
    • 0021871375 scopus 로고
    • A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules
    • Goodford, P. J. A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules J. Med. Chem. 1985, 28, 849-857 10.1021/jm00145a002
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 23
    • 0033047007 scopus 로고    scopus 로고
    • SuperStar: A Knowledge-Based Approach for Identifying Interaction Sites in Proteins
    • Verdonk, M. L.; Cole, J. C.; Taylor, R. SuperStar: A Knowledge-Based Approach for Identifying Interaction Sites in Proteins J. Mol. Biol. 1999, 289, 1093-1108 10.1006/jmbi.1999.2809
    • (1999) J. Mol. Biol. , vol.289 , pp. 1093-1108
    • Verdonk, M.L.1    Cole, J.C.2    Taylor, R.3
  • 24
    • 33845413241 scopus 로고    scopus 로고
    • Determination of the Sequence Specificity of XIAP BIR Domains by Screening a Combinatorial Peptide Library
    • Sweeney, M. C.; Wang, X.; Park, J.; Liu, Y.; Pei, D. Determination of the Sequence Specificity of XIAP BIR Domains by Screening a Combinatorial Peptide Library Biochemistry 2006, 45, 14740-14748 10.1021/bi061782x
    • (2006) Biochemistry , vol.45 , pp. 14740-14748
    • Sweeney, M.C.1    Wang, X.2    Park, J.3    Liu, Y.4    Pei, D.5
  • 26
    • 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
  • 27
    • 0025916872 scopus 로고
    • Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method
    • Miranker, A.; Karplus, M. Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method Proteins: Struct., Funct., Genet. 1991, 11, 29-34 10.1002/prot.340110104
    • (1991) Proteins: Struct., Funct., Genet. , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 28
    • 0036715931 scopus 로고    scopus 로고
    • Pyridinylimidazole Based P38 MAP Kinase Inhibitors
    • Jackson, P. F.; Bullington, J. L. Pyridinylimidazole Based P38 MAP Kinase Inhibitors Curr. Top. Med. Chem. 2002, 2, 1011-1020 10.2174/1568026023393372
    • (2002) Curr. Top. Med. Chem. , vol.2 , pp. 1011-1020
    • Jackson, P.F.1    Bullington, J.L.2
  • 30
    • 0031552362 scopus 로고    scopus 로고
    • Development and Validation of a Genetic Algorithm for Flexible Docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking J. Mol. Biol. 1997, 267, 727-748 10.1006/jmbi.1996.0897
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 31
    • 62449330667 scopus 로고    scopus 로고
    • Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
    • Korb, O.; Stutzle, T.; Exner, T. E. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS J. Chem. Inf. Model. 2009, 49, 84-96 10.1021/ci800298z
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 84-96
    • Korb, O.1    Stutzle, T.2    Exner, T.E.3
  • 36
    • 84979886817 scopus 로고    scopus 로고
    • Special Issue: "A Snapshot in Time: Docking Challenge" Issue; Springer, Vol. Issue.
    • Special Issue: "A Snapshot in Time: Docking Challenge": Journal of Computer-Aided Molecular Design; Warren, G. L., Issue Ed.; Springer, 2012; Vol. 26, Issue 6.
    • (2012) Journal of Computer-Aided Molecular Design , vol.26 , Issue.6
    • Warren, G.L.1
  • 39
    • 84865271039 scopus 로고    scopus 로고
    • Variability in Docking Success Rates Due to Dataset Preparation
    • Corbeil, C. R.; Williams, C. I.; Labute, P. Variability in Docking Success Rates Due to Dataset Preparation J. Comput.-Aided Mol. Des. 2012, 26, 775-786 10.1007/s10822-012-9570-1
    • (2012) J. Comput.-Aided Mol. Des. , vol.26 , pp. 775-786
    • Corbeil, C.R.1    Williams, C.I.2    Labute, P.3
  • 40
    • 84865212063 scopus 로고    scopus 로고
    • Docking Performance of the Glide Program as Evaluated on the Astex and DUD Datasets: A Complete Set of Glide SP Results and Selected Results for a New Scoring Function Integrating Watermap and Glide
    • Repasky, M. P.; Murphy, R. B.; Banks, J. L.; Greenwood, J. R.; Tubert-Brohman, I.; Bhat, S.; Friesner, R. A. Docking Performance of the Glide Program as Evaluated on the Astex and DUD Datasets: A Complete Set of Glide SP Results and Selected Results for a New Scoring Function Integrating Watermap and Glide J. Comput.-Aided Mol. Des. 2012, 26, 787-799 10.1007/s10822-012-9575-9
    • (2012) J. Comput.-Aided Mol. Des. , vol.26 , pp. 787-799
    • Repasky, M.P.1    Murphy, R.B.2    Banks, J.L.3    Greenwood, J.R.4    Tubert-Brohman, I.5    Bhat, S.6    Friesner, R.A.7
  • 42
    • 84938150763 scopus 로고    scopus 로고
    • Flexaid: Revisiting Docking on Non-Native-Complex Structures
    • Gaudreault, F.; Najmanovich, R. J. Flexaid: Revisiting Docking on Non-Native-Complex Structures J. Chem. Inf. Model. 2015, 55, 1323-1336 10.1021/acs.jcim.5b00078
    • (2015) J. Chem. Inf. Model. , vol.55 , pp. 1323-1336
    • Gaudreault, F.1    Najmanovich, R.J.2
  • 44
    • 84864264343 scopus 로고    scopus 로고
    • Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
    • Mysinger, M. M.; Carchia, M.; Irwin, J. J.; Shoichet, B. K. Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking J. Med. Chem. 2012, 55, 6582-6594 10.1021/jm300687e
    • (2012) J. Med. Chem. , vol.55 , pp. 6582-6594
    • Mysinger, M.M.1    Carchia, M.2    Irwin, J.J.3    Shoichet, B.K.4
  • 45
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking Sets for Molecular Docking
    • Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking Sets for Molecular Docking J. Med. Chem. 2006, 49, 6789-6801 10.1021/jm0608356
    • (2006) J. Med. Chem. , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 46
    • 84865266975 scopus 로고    scopus 로고
    • Pose Prediction and Virtual Screening Performance of GOLD Scoring Functions in a Standardized Test
    • Liebeschuetz, J. W.; Cole, J. C.; Korb, O. Pose Prediction and Virtual Screening Performance of GOLD Scoring Functions in a Standardized Test J. Comput.-Aided Mol. Des. 2012, 26, 737-748 10.1007/s10822-012-9551-4
    • (2012) J. Comput.-Aided Mol. Des. , vol.26 , pp. 737-748
    • Liebeschuetz, J.W.1    Cole, J.C.2    Korb, O.3
  • 47
    • 84893388298 scopus 로고    scopus 로고
    • Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment
    • Zhang, X.; Wong, S. E.; Lightstone, F. C. Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment J. Chem. Inf. Model. 2014, 54, 324-337 10.1021/ci4005145
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 324-337
    • Zhang, X.1    Wong, S.E.2    Lightstone, F.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.