Ligand Identification Scoring Algorithm (LISA)

Journal of Chemical Information and Modeling

Volumn 51, Issue 6, 2011, Pages 1296-1306

  Zheng, Zheng ^a   Merz, Kenneth M ^a  

^a University of Florida ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHELATION; COMPLEX NETWORKS; COMPLEXATION; EQUILIBRIUM CONSTANTS; FREE ENERGY; HYDROGEN BONDS; LIGANDS; PROTEINS; VAN DER WAALS FORCES;

BINDING FREE ENERGY; DISSOCIATION EQUILIBRIA; H-BONDING INTERACTION; LIGAND BINDING AFFINITY; PROTEIN-LIGAND BINDING AFFINITIES; PROTEIN-LIGAND COMPLEXES; SCORING ALGORITHMS; THREE-DIMENSIONAL STRUCTURE;

BINDING ENERGY;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; CHEMICAL STRUCTURE; CONFORMATION; DRUG DESIGN; HYDROGEN BOND; INFORMATION SCIENCE; METABOLISM; METHODOLOGY; REPRODUCIBILITY; THERMODYNAMICS;

ALGORITHMS; DRUG DESIGN; HYDROGEN BONDING; INFORMATICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NEURAL NETWORKS (COMPUTER); PROTEINS; REPRODUCIBILITY OF RESULTS; THERMODYNAMICS;

EID: 79959765741     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci2000665     Document Type: Article

References (55)

1. Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. BindingDB: A Web-Accessible Database of Experimentally Determined Protein-Ligand Binding Affinities Nucleic Acids Res. 2007, 35, 198-201
2. Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent Developments in Fragment-Based Drug Discovery J. Med. Chem. 2008, 51, 3661-3680 (Pubitemid 351956496)
3. Mobley, D. L.; Dill, K. A. Binding of Small-Molecule Ligands to Proteins: "What You See" Is Not Always "What You Get Structure 2009, 17, 489-498
4. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 2001, 46, 3-26 (Pubitemid 33653411)
5. Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26 (Pubitemid 34855041)
6. Merz, K. M. Limits of Free Energy Computation for Protein-Ligand Interactions J. Chem. Theory Comput. 2010, 6, 1769-1776
7. Kolb, P.; Irwin, J. J. Docking Screens: Right for the Right Reasons? Curr. Top. Med. Chem. 2009, 9, 755-770
8. Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases J. Comput.-Aided Mol. Des. 2001, 15, 411-428 (Pubitemid 32452109)
9. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662 (Pubitemid 128590223)
10. Weiner, S. J.; Kollman, P. A.; Case, D. A. A new force field for molecular mechanical simulation of nucleic acids and proteins J. Am. Chem. Soc. 1984, 106, 765-784
11. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An all atom force field for simulations of proteins and nucleic acids J. Comput. Chem. 1986, 7, 230-252
12. 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 (Pubitemid 29136170)
13. Muegge, I. A knowledge-based scoring function for protein-ligand interactions: Probing the reference state Perspect. Drug Discovery Des. 2000, 20, 99-114
14. Muegge, I. Effect of ligand volume correction on PMF scoring J. Comput. Chem. 2001, 22, 418-425 (Pubitemid 33640780)
15. Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions J. Mol. Biol. 2000, 295, 337-356 (Pubitemid 30045364)
16. Ishchenko, A. V.; Shakhnovich, E. I. Small molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions J. Med. Chem. 2002, 45, 2770-2780 (Pubitemid 34627647)
17. Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Thornton, J. M. BLEEP-potential of mean force describing protein-ligand interactions: I. Generating potential J. Comput. Chem. 1999, 20, 1165-1176 (Pubitemid 129651749)
18. CSD- knowledgebased scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction J. Med. Chem. 2005, 48, 6296-6303 (Pubitemid 41428984)
19. Huang, S.-Y.; Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function J. Comput. Chem. 2006, 27, 1876-1882 (Pubitemid 44672569)
20. Huang, S.-Y.; Zou, X. Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions J. Chem. Inf. Model. 2010, 50, 262-273
21. Jones, G.; Wilett, 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 (Pubitemid 27170693)
22. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A. A Fast Flexible Docking Method using an Incremental Construction Algorithm J. Mol. Biol. 1996, 261, 470-489 (Pubitemid 26335901)
23. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy J. Med. Chem. 2004, 47, 1739-1749 (Pubitemid 38380917)
24. Wang, R.; Liu, L.; Lai, L.; Tang, Y. SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex J. Mol. Model. 1998, 4, 379-394 (Pubitemid 128664733)
25. Korb, O.; Stützle, T.; Exner, T. E. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS J. Chem. Inf. Model. 2009, 49, 84-96
26. Teramoto, R.; Fukunishi, H. Supervised Consensus Scoring for Docking and Virtual Screening J. Chem. Inf. Model. 2007, 47, 526-534 (Pubitemid 46615954)
27. Deng, Y.; Roux, B. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 2234-2246
28. Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind Database: Methodologies and Updates J. Med. Chem. 2005, 48, 4111-4119 (Pubitemid 40800619)
29. Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures J. Med. Chem. 2004, 47, 2977-2980 (Pubitemid 38702694)
30. Søndergaard, C. R.; Garrett, A. E.; Carstensen, T.; Pollastri, G.; Nielsen, J. E. Structural Artifacts in Protein-Ligand X-ray Structures: Implications for the Development of Docking Scoring Functions J. Med. Chem. 2009, 52, 5673-5684
31. Böhm, 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
32. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197
33. Vedani, A. YETI: An interactive molecular mechanics program for small-molecule protein complexes J. Comput. Chem. 2004, 9, 269-280
34. Vedani, A.; Dunitz, J. D. Lone-pair directionality in hydrogen-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides J. Am. Chem. Soc. 1985, 107, 7653-7658 (Pubitemid 16185242)
35. Martin, Y. C. Let's not forget tautomers J. Comput.-Aided Mol. Des. 2009, 23, 693-704
36. Sarkhel, S.; Desiraju, G. R. N-H...O, O-H...O, and C-H...O hydrogen bonds in protein-ligand complexes: Strong and weak interactions in molecular recognition Proteins: Struct., Funct., Bioinf. 2004, 54, 247-259 (Pubitemid 38084066)
37. Connolly, M. L. The molecular surface package J. Mol. Graphics 1993, 11, 139-141 (Pubitemid 23200921)
38. Huang, S. -Y.; Kuntz, I. D.; Zou, X. Pairwise GB/SA Scoring Function for Structure-based Drug Design J. Phys. Chem. B 2004, 108, 5453-5462
39. Vedani, A.; Huhta, D. W. A new force field for modeling metalloproteins J. Am. Chem. Soc. 1990, 112, 4759-4767 (Pubitemid 20285913)
40. Wang, R.; Fu, Y.; Lai, L. A New Atom-Additive Method for Calculating Partition Coefficients J. Chem. Inf. Comput. Sci. 1997, 37, 615-621 (Pubitemid 127603572)
41. Wang, R.; Lu, Y.; Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking J. Med. Chem. 2003, 46, 2287-2303 (Pubitemid 36637914)
42. Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. A Knowledge-Based Energy Function for Protein-Ligand, Protein-Protein, and Protein-DNA Complexes J. Med. Chem. 2005, 48, 2325-2335 (Pubitemid 40516427)
43. Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, D. B.; Freer, S. T. Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming Chem. Biol. 1995, 2, 317-324
44. Gehlhaar, D. K.; Bouzida, D.; Rejto, P. A. In Rational Drug Design: Novel Methodology and Practical Applications; Parrill, L.; Reddy, M. R., Eds.; American Chemical Society: Washington, DC, 1999; Vol. 719, pp 292-311.
45. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Talor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748 (Pubitemid 27170693)
46. Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy approach to macromolecule-ligand interactions J. Comput. Chem. 1992, 13, 505-524
47. 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 (Pubitemid 127505895)
48. Böhm, H. J. Prediction of binding constants of ptotein ligands: A fast method for the polarization of hits obtained from de novo design or 3D database search programs J. Comput.-Aided Mol. Des. 1998, 12, 309-323
49. CERIUS2 LigandFit User Manual; Accelrys Inc.: San Diego, CA, 2000; pp 3-48.
50. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 1996, 261, 470-489 (Pubitemid 26335901)
51. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662 (Pubitemid 128590223)
52. Nobeli, I.; Mitchell, J. B. O.; Alex, A.; Thornton, J. M. Evaluation of a knowledge-based potential of mean force for scoring docked proteinligand complexes J. Comput. Chem. 2001, 22, 673-688 (Pubitemid 32442164)
53. DeWitte, R. S.; Shakhnovich, E. I. SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence J. Am. Chem. Soc. 1996, 118, 11733-11744 (Pubitemid 26417462)
54. Wang, R.; Lu, Y.; Fang, X.; Wang, S. An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes J. Chem. Inf. Comput. Sci. 2004, 44, 2114-2125
55. Hu, L.; Benson, M. L.; Smith, R. D.; Lerner, M. G.; Carlson, H. A. Binding MOAD (Mother Of All Databases) Proteins 2005, 60, 333-400