Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry

PLoS ONE

Volumn 2, Issue 6, 2007, Pages

  Wang, Qi ^a   Pang, Yuan Ping ^a  

^a MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CRYSTALLIZATION; FACTUAL DATABASE; HUMAN; METABOLISM; PROTEIN CONFORMATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; HUMANS; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 40749159291     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000531     Document Type: Article

References (21)

1. Allen FH, (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr Sect B: Struct Sci 58: 380-388.
2. DesJarlais RL, Seibel GL, Kuntz ID, Furth PS, Alvarez JC, et al.(1990) Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci USA 87: 6644-6648.
3. Pang Y-P, Perola E, Xu K, Prendergast FG, (2001) EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J Comput Chem 22: 1750-1771.
4. Pang YP, (2007) In silico drug discovery: solving the "target-rich and lead-poor" imbalance using the genome-to-drug-lead paradigm. Clin Pharmacol Ther 81: 30-34.
5. Pang Y-P, Mullins T, Swartz B, McAllister J, Smith B, et al.(2007) EUDOC on Blue Gene: accelerating the transfer of drug discoveries from laboratory to patient. IBM J Res Dev in press.
6. Perola E, Xu K, Kollmeyer TM, Kaufmann SH, Prendergast FG, et al.(2000) Successful virtual screening of a chemical database for farnesyltransferase inhibitor leads. J Med Chem 43: 401-408.
7. Miller MA, (2002) Chemical database techniques in drug discovery. Nat Rev Drug Discov 1: 220-227.
8. Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, et al.(1997) Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A. Nat Struct Biol 4: 57-63.
9. Pang Y-P, Xu K, Kollmeyer TM, Perola E, McGrath WJ, et al.(2001) Discovery of a new inhibitor lead of adenovirus proteinase: steps toward selective, irreversible inhibitors of cysteine proteinases. FEBS Lett 502: 93-97.
10. Sun H, Pang YP, Lockridge O, Brimijoin S, (2002) Re-engineering butyrylcholinesterase as a cocaine hydrolase. Mol Pharmacol 62: 220-224.
11. Dooley AJ, Shindo N, Taggart B, Park JG, Pang Y-P, (2006) From genome to drug lead: identification of a small-molecule inhibitor of the SARS virus. Bioorg Med Chem Lett 16: 830-833.
12. Park JG, Sill PC, Makiyi EF, Garcia-Sosa AT, Millard CB, et al.(2006) Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A. Bioorg Med Chem 14: 395-408.
13. Lehn JM, (1993) Supramolecular chemistry. Science 260: 1762-1763.
14. Eyal E, Gerzon S, Potapov V, Edelman M, Sobolev V, (2005) The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J Mol Biol 351: 431-442.
15. Pascal RA, Ho DM, (1993) Molecular-sructure of Rebek diacid quinoxaline- confirmation of 2-point binding. J Am Chem Soc 115: 8507-8508.
16. Duffy EM, Jorgensen WL, (1994) Structure and binding for complexes of Rebek's acridine diacid with pyrazine, quinoxaline, and pyridine from Monte Carlo simulations with an all-atom force field. J Am Chem Soc 116: 6337-6343.
17. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, et al.(1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179-5197.
18. Rebek J Jr, Nemeth D, (1986) Molecular recognition: Ionic and aromatic stacking interactions bind complementary functional groups in a molecular cleft. J Am Chem Soc 108: 5637-5638.
19. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE III, et al.(1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 91: 1-41.
20. Cieplak P, Cornell WD, Bayly C, Kollman PA, (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. J Comput Chem 16: 1357-1377.
21. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al.(2004) Gaussian 03, Revision C.02. Gaussian, Inc, Wallingford CT.