AutoMap: A tool for analyzing protein-ligand recognition using multiple ligand binding modes

Journal of Molecular Graphics and Modelling

Volumn 40, Issue , 2013, Pages 80-90

  Agostino, Mark ^a,b   Mancera, Ricardo L ^a   Ramsland, Paul A ^a,b,c,d   Yuriev, Elizabeth ^b  

^a CURTIN UNIVERSITY   (Australia)

^b MONASH UNIVERSITY   (Australia)

^c BURNET INSTITUTE   (Australia)

^d UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Hot spotting; Interaction fingerprinting; Molecular docking; Protein ligand recognition; Site mapping

Indexed keywords

AUTOMATED PROCEDURES; HOT SPOTTING; INTERACTION FINGERPRINTING; LIGAND RECOGNITION; LIGAND-BINDING RESIDUES; MAPPING TECHNIQUES; MOLECULAR DOCKING; MOST LIKELY; MULTIPLE LIGANDS; PERL SCRIPTS; PROTEIN RESIDUES; PROTEIN-BINDING SITES; PROTEIN-LIGAND RECOGNITION; RAPID OPTIMIZATION; SITE MAP; STRUCTURE-BASED DRUG DESIGN; TARGET PROTEINS; TEST CASE; VAN DER WAALS INTERACTIONS;

AUTOMATION; BINDING ENERGY; BIOCHEMISTRY; CARBOHYDRATES; FORECASTING; HYDROGEN BONDS; MAPPING; MOLECULAR MODELING; OPTIMIZATION; PROTEINS; VAN DER WAALS FORCES;

LIGANDS;

CARBOHYDRATE; LIGAND; PEPTIDE; PROTEIN;

ANTIGEN BINDING; ARTICLE; AUTOMAP; AUTOMATION; BINDING SITE; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN CARBOHYDRATE INTERACTION;

ANTIBODIES; BINDING SITES; CARBOHYDRATES; COMPUTER SIMULATION; DRUG DESIGN; HYDROGEN BONDING; LECTINS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PEPTIDES; PROTEIN BINDING; PROTEINS; SOFTWARE;

EID: 84873034177     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.01.001     Document Type: Article

References (51)

1. E. Yuriev, M. Agostino, and P.A. Ramsland Challenges and advances in computational docking: 2009 in review Journal of Molecular Recognition 24 2011 149 164
2. P.J. Lewi, M. de Jonge, F. Daeyaert, L. Foymans, M. Vinkers, and J. Heeres On the detection of multiple-binding modes of ligands to proteins from biological, structural and modeling data Journal of Computer-Aided Molecular Design 17 2003 129 134
3. B. Gorelik, and A. Goldblum High quality binding modes in docking ligands to proteins Proteins 71 2008 1373 1386
4. K.M. Campbell, and K.J. Lumb Structurally distinct modes of recognition of the KIX domain of CBP by Jun and CREB Biochemistry 41 2002 13956 13964
5. M.R. Wester, E.F. Johnson, C. Marques-Soares, P.M. Dansette, D. Mansuy, and C.D. Stout Structure of a substrate complex of mammalian cytochrome P4502C5 at 2.3 angstrom resolution: evidence for multiple substrate binding modes Biochemistry 42 2003 6370 6379
6. M.D. Jacobs, J. Black, O. Futer, L. Swenson, B. Hare, and M. Fleming Pim-1 ligand-bound structures reveal the mechanism of serine/threonine kinase inhibition by LY294002 Journal of Biological Chemistry 280 2005 13728 13734
7. 2A receptor in complex with ZM241385 and the xanthines XAC and caffeine Structure 19 2011 1283 1293
8. R.E. Watkins, G.B. Wisely, L.B. Moore, J.L. Collins, M.H. Lambert, and S.P. Williams The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity Science 292 2001 2329 2333
9. P. Källblad, R.L. Mancera, and N.P. Todorov Assessment of multiple binding modes in ligand-protein docking Journal of Medicinal Chemistry 47 2004 3334 3337
10. E. Yuriev, P.A. Ramsland, and A.B. Edmunson Docking of combinatorial peptide libraries into a broadly cross-reactive human IgM Journal of Molecular Recognition 14 2001 172 184
11. E. Yuriev, P.A. Ramsland, and A.B. Edmundson Recognition of IgG-derived peptides by a human IgM with an unusual combining site Scandinavian Journal of Immunology 55 2002 242 255
12. M. Agostino, M.S. Sandrin, P.E. Thompson, E. Yuriev, and P.A. Ramsland In silico analysis of antibody-carbohydrate interactions and its application to xenoreactive antibodies Molecular Immunology 47 2009 233 246
13. M. Agostino, E. Yuriev, and P.A. Ramsland A computational approach for exploring carbohydrate recognition by lectins in innate immunity Frontiers in Immunology 2 2011 23
14. J. Milland, E. Yuriev, P.-X. Xing, I.F.C. McKenzie, P.A. Ramsland, and M.S. Sandrin Carbohydrate residues downstream of the terminal Galα(1,3)Gal epitope modulate the specificity of xenoreactive antibodies Immunology and Cell Biology 85 2007 623 632
15. M. Agostino, M.S. Sandrin, P.E. Thompson, P.A. Ramsland, and E. Yuriev Peptide inhibitors of xenoreactive antibodies mimic the interaction profile of the native carbohydrate antigens Biopolymers 96 2011 193 206
16. E. Yuriev, M.S. Sandrin, and P.A. Ramsland Antibody-ligand docking: insights into peptide-carbohydrate mimicry Molecular Simulation 34 2008 461 468
17. M. Agostino, M.S. Sandrin, P.E. Thompson, E. Yuriev, and P.A. Ramsland Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps Glycobiology 20 2010 724 735
18. Worldwide Protein Data Bank Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.30 2011
19. A.C. Wallace, R.A. Laskowski, and J.M. Thornton LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Engineering 8 1995 127 134
20. D.K. Chalmers, and B.P. Roberts Silico-A Perl Molecular Modelling Toolkit 2011
21. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Kilcic, and D.T. Mainz Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy Journal of Medicinal Chemistry 2004 1739 1749
22. Schrödinger, LLC. Glide, Version 5.6, New York, NY, 2010.
23. M.L. Verdonk, J.C. Cole, M.J. Hartshorn, C.W. Murray, and R.D. Taylor Improved protein-ligand docking using GOLD Proteins 52 2003 609 623
24. P.T. Lang, S.R. Brozell, S. Mukherjee, E.F. Pettersen, E.C. Meng, and V. Thomas DOCK 6: combining techniques to model RNA-small molecule complexes RNA 15 2009 1219 1230
25. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, and R.K. Belew Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function Journal of Computational Chemistry 19 1998 1639 1662
26. R.A. Laskowski, and M.B. Swindells LigPlot+: multiple ligand-protein interaction diagrams for drug discovery Journal of Chemical Information and Modeling 51 2011 2778 2786
27. F.M. McRobb, B. Capuano, I.T. Crosby, D.K. Chalmers, and E. Yuriev Homology modeling and docking evaluation of aminergic G protein-coupled receptors Journal of Chemical Information and Modeling 50 2010 626 637
28. M. Agostino, P.A. Ramsland, and E. Yuriev Antibody recognition of cancer-related gangliosides and their mimics investigated using in silico site mapping PLoS ONE 7 2012 e35457
29. M. Agostino, C. Jene, T. Boyle, P.A. Ramsland, and E. Yuriev Molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures Journal of Chemical Information and Modeling 49 2009 2749 2760
30. R. Brenke, D. Kozakov, G.-Y. Chuang, D. Beglov, D. Hall, and M.R. Landon Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques Bioinformatics 25 2009 621 627
31. M. Agostino, W. Farrugia, M.S. Sandrin, A.M. Scott, E. Yuriev, and P.A. Ramsland Structural glycobiology of antibody recognition in xenotransplantation and cancer immunotherapy P. Kosma, S. Müller-Loennies, Anticarbohydrate Antibodies-From Molecular Basis to Clinical Application 2012 Springer New York 203 228
32. M. Agostino, M.S. Sandrin, P.E. Thompson, W. Farrugia, P.A. Ramsland, and E. Yuriev Carbohydrate-mimetic peptides: structural aspects of mimicry and therapeutic implications Expert Opinion on Biological Therapy 11 2011 211 224
33. F.-X. Theillet, F.A. Saul, B. Vuillez-Le Normand, S. Hoos, F. Felici, and A. Weintraub Structural mimicry of O-antigen by a peptide revealed in a complex with an antibody raised against Shigella flexneri serotype 2a Journal of Molecular Biology 388 2009 839 850
34. N.K. Vyas, M.N. Vyas, M.C. Chervenak, D.R. Bundle, B.M. Pinto, and F.A. Quiocho Structural basis of peptide-carbohydrate mimicry in an antibody-combining site Proceedings of the National Academy of Sciences of the United States of America 100 2003 15023 15028
35. P.J. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules Journal of Medicinal Chemistry 28 1985 849 857
36. A. Miranker, and M. Karplus Functionality maps of binding sites: a multiple copy simultaneous search method Proteins 11 1991 29 34
37. P.D.J. Grootenhuis, and M. Karplus Functionality map analysis of the active site cleft of human thrombin Journal of Computer-Aided Molecular Design 10 1996 1 10
38. M.R. Landon, D.R. Lancia Jr., J. Yu, S.C. Thiel, and S. Vajda Identification of hot spots within druggable binding regions by computational solvent mapping of proteins Journal of Medicinal Chemistry 50 2007 1231 1240
39. Y. Gao, R.X. Wang, and L.H. Lai Structure-based method for analyzing protein-protein interfaces Journal of Molecular Modeling 10 2004 44 54
40. J. Fernandez-Recio, M. Totrov, C. Skorodumov, and R. Abagyan Optimal Docking Area: a new method for predicting protein-protein interaction sites Proteins 58 2005 134 143
41. H. Shadnia, J.S. Wright, and J.M. Anderson Interaction force diagrams: new insight into ligand-receptor binding Journal of Computer-Aided Molecular Design 23 2009 185 194
42. M.L. Verdonk, J.C. Cole, P. Watson, V. Gillet, P. Willett, and SuperStar: Improved knowledge-based interaction fields for protein binding sites Journal of Molecular Biology 307 2001 841 859
43. M.L. Verdonk, J.C. Cole, and R. Taylor SuperStar: a knowledge-based approach for identifying interaction sites in proteins Journal of Molecular Biology 289 1999 1093 1108
44. M.D. Kelly, and R.L. Mancera A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein Journal of Computer-Aided Molecular Design 17 2003 401 414
45. M.D. Kelly, and R.L. Mancera A new method for estimating the importance of hydrophobic groups in the binding site of a protein Journal of Medicinal Chemistry 48 2005 1069 1078
46. M.D. Kelly, and R.L. Mancera Comparative analysis of the surface interaction properties of the binding sites of CDK2, CDK4 and ERK2 ChemMedChem 1 2006 366 375
47. S.C. Brewerton The use of protein-ligand interaction fingerprints in docking Current Opinion in Drug Discovery and Development 11 2008 356 364
48. M.D. Kelly, and R.L. Mancera Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based design Journal of Chemical Information and Computer Science 44 2004 1942 1951
49. J. Singh, Z. Deng, G. Narale, and C. Chuaqui Structural interaction fingerprints: a new approach to organizing, mining, analyzing and designing protein-small molecule complexes Chemical Biology & Drug Design 67 2006 5 12
50. S. Sciabola, R.V. Stanton, J.E. Mills, M.M. Flocco, M. Baroni, and G. Cruciani High-throughput virtual screening of proteins using GRID molecular interaction fields Journal of Chemical Information and Modeling 50 2010 155 169
51. T. Sato, T. Honma, and S. Yokoyama Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening Journal of Chemical Information and Modeling 50 2010 170 185