Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education

In Silico Biology

Volumn 11, Issue 1-2, 2011, Pages 41-60

  Guha, Rajarshi ^a   Wiggins, Gary D ^a   Wild, David J ^a   Baik, Mu Hyun ^a   Pierce And, Marlon E ^b   Fox, Geoffrey C ^a  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; COOPERATION; EDUCATION; FACTUAL DATABASE; INFORMATION SCIENCE; INTERNET; UNIVERSITY;

CHEMISTRY; COOPERATIVE BEHAVIOR; DATABASES, FACTUAL; INFORMATICS; INTERNET; SOFTWARE; UNIVERSITIES;

EID: 84859531430     PISSN: 14343207     EISSN: None     Source Type: Journal    
DOI: 10.3233/CI-2008-0015     Document Type: Article

References (63)

1. Chemical Information Sources Wiki, http://cheminfo.informatics.indiana. edu/cicc/cis (Accessed April 17, 2007).
2. OpenEye, http://www.eyesopen.com (Accessed April 17, 2007).
3. IdeaConsult Ltd., http://ecb.jrc.it/qsar/home.php?CONTENU=/qsar/qsar- tools/qsar tools toxtree.php (Accessed Apr 17, 2007).
4. Knime, http://www.knime.org (Accessed April 17, 2007).
5. Scitegic Pipeline Pilot, http://www.scitegic.com (Accessed April 17, 2007).
6. UNC Informatics Survey, http://ils.unc.edu/informatics programs/ (Accessed April 17, 2007).
7. Obernai Declaration, http://infochim.u-strasbg.fr/chemoinfor-matics/ Obernai declaration.php (AccessedApril 17, 2007).
8. D.K. Agrafiotis, W. Cedeno and V.S. Lobanov, On the Use of Neural Network Ensembles in QSAR and QSPR, J Chem Inf Comput Sci 42 (2002), 903-911. (Pubitemid 35355240)
9. J. Alameda, M. Christie, G.C. Fox, J. Futrelle, D. Gannon, M. Hategan, G. Kandaswamy, G. von Laszewski, M.A. Nacar, M.E. Pierce, E. Roberts, C. Severance and M. Thomas, The Open Grid Computing Environments collaboration: Portlets and services for science gateways. Published Online: 10 Oct 2006 DOI: 10.1002/cpe.1078. Available from http://www3.interscience.wiley.com/cgi-bin/ fulltext/113391287/PDFSTART 2006.
10. D. Atkins, Report of Blue-Ribbon Advisory Panel on Cyberinfrastructure, National Science Foundation, 2004.
11. M.P.Atkinson, D.De Roure, A.N.Dunlop, G.C. Fox, P.Henderson, A.J.G.Hey, N.W. Paton, S.Newhouse, S. Parastatidis, A.E. Trefethen, P.Watson and J.Webber,Web Service Grids: An evolutionary approach, Concurrency and Computation: Practice and Experience 18(10) (2005), 1009-1019.
12. M.A. Avery, M. Alvim-Gaston, C.R. Rodrigues, E.J. Barreiro, F.E. Cohen, Y.A. Sabnis and J.R. Woolfrey, Structure Activity Relationships of the Antimalarial Agent Artemisinin. The Development of Predictive in Vitro Potency Models Using CoMFA and HQSAR Methodologies, J Med Chem 45 (2002), 292-303. (Pubitemid 34073448)
13. B.C. Bailey, H. Fan, J.C. Huffman, M.H. Baik, D.J. Mindiola, Room temperature ring-opening metathesis of pyridines by a transient Ti C linkage, Journal of the American Chemical Society 128(21) (2006), 6798-6799. (Pubitemid 43830562)
14. S.C. Basak, D.R.Mills, A.T. Balaban and B.D. Gute, Prediction ofMutagenicity of Aromatic and Heteroaromatic Amines from Structure: A Hierarchical QSAR Approach, J Chem Inf Comput Sci 41 (2001), 671-678.
15. F. Berman, G.C. Fox and T. Hey, Grid Computing: Making the Global Infrastructure a Reality, John Wiley & Sons: Chichester, England, 2003.
16. M. Bohl, J. Dunbar, E.M. Gifford, T. Heritage, D. Wild, P. Willett and D.J. Wilton, Scaffold Searching: Automated Identification of Similar Ring Systems for the Design of Combinatorial Libraries, Quantitative Structure-Actitivy Releationships 21(6) (2002), 590-597. (Pubitemid 36216058)
17. L. Breiman, J.H. Friedman, R.A. Olshen and C.J. Stone, Classification and Regression Trees, Chapman & Hall/CRC: Boca Raton, FL, 1984.
18. A.L. Bremet, Cyberinfrastructure: The Second Revolution, The Chronicle of Higher Education 53(18) (2007), B5.
19. F. Brown, Chemoinformatics - A ten year update. Current Opinion in Drug Discovery and Development 8(3) (2005), 298-302.
20. D. Butina and J.M.R. Gola, Modeling Aqueous Solubility, J Chem Inf Comput Sci 43 (2003), 837-841.
21. G.M. Cramer, R.A. Ford and R.L. Hall, Estimation of Toxic Hazard - A Decision Tree Approach, Food Cosmet Toxicol 16(3) (1978), 255-276. (Pubitemid 9010193)
22. R.D. Cramer, R.J. Jilek, S. Guessregen, S.J. Clark, B. Wendt and R.D. Clark, Lead Hopping. Validation of Topomer Similarity as a Superior Predictor of Similar Biological Activities, J Med Chem 47 (2004), 6777-6791. (Pubitemid 40053766)
23. T.G. Dietterich, The Handbook of Brain Theory and Neural Networks, in M.A. Arbib, ed., MIT Press: Cambridge, MA, 2002.
24. X. Dong, K.E. Gilbert, R. Guha, R. Heiland, J. Kim, M.E. Pierce, G.C. Fox and D.J. Wild, A web service infrastructure for chemoinformatics, Journal of Chemical Information and Modeling (2007), Submitted.
25. D. Dutta, R. Guha, P.C. Jurs and T. Chen, Scalable Partitioning and Exploration of Chemical Spaces using Geometric Hashing, J Chem Inf Model 46 (2006), 321-333. (Pubitemid 43282125)
26. D. Dutta, R. Guha, D.Wild and T. Chen, Ensemble Feature Selection: Consistent Descriptor Subsets forMultiple QSAR Models, J Chem Inf Model (2007), ASAP.
27. I. Foster and C. Kesselman, The Grid 2: Blueprint for a New Computing Infrastructure, Morgan Kaufmann: 2004.
28. A.R. Fout, F. Basuli, H.J. Fan, J. Tomaszewski, J.C. Huffman, M.H. Baik and D.J. Mindiola, A Co2N2 diamond-core resting state of cobalt(I): A three-coordinate Co-I synthon invoking an unusual pincer-type rearrangement, Angewandte Chemie-International Edition 45(20) (2006), 3291-3295. (Pubitemid 44098992)
29. G.C. Fox and D. Gannon, Special Issue: Workflow in Grid Systems, Concurrency and Computation: Practice and Experience 18(10) (2006), 1009-1019. (Pubitemid 44268986)
30. P. Graham, Web 2.0. http://www.paulgraham.com/web20.html (Accessed April 17, 2007), 2005.
31. R. Guha, D. Dutta, P.C. Jurs and T. Chen, RNN curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method, J Chem Inf Model 46(4) (2006), 1713-1722. (Pubitemid 44185696)
32. R. Guha and P.C. Jurs, Determining the Validity of a QSAR model-A Classification Approach, J Chem Inf Model 45(1)(2005), 65-73. (Pubitemid 40736957)
33. R. Guha and P.C. Jurs, Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance, J Chem Inf Model 45 (2005), 800-806. (Pubitemid 40795183)
34. R. Guha and P.C. Jurs, The Development of Linear, Ensemble and Non-linear Models for the Prediction and Interpretation of the Biological Activity of a Set of PDGFR Inhibitors, J Chem Inf Comput Sci 44 (2004), 2179-2189.
35. R. Guha and P.C. Jurs, The Development of QSARModels To Predict and Interpret the Biological Activity of Artemisinin Analogues, J Chem Inf Comp Sci 44 (2004), 1440-1449.
36. R.Guha,D.T. Stanton and P.C. Jurs, InterpretingComputationalNeuralNetworkQSARModels: ADetailed Interpretation of the Weights and Biases, J Chem Inf Model 45 (2005), 1109-1121. (Pubitemid 41156711)
37. T.A. Halgren, Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94, J Comp Chem 17 (1996), 490-519.
38. C. Hansch, A Quantitative Approach to Biochemical Structure-Activity Relationships, Acc Chem Res 2 (1969), 232-239.
39. D.M. Hawkins, The problem of overfitting, J Chem Inf Comput Sci 44(1) (2004), 1-12.
40. R. Kohavi and G.H. John, Wrappers for Feature Subset Selection, Artif Intell 97(1-2) (1997), 273-324. (Pubitemid 127401107)
41. M.H. Lim, B.A. Wong, W.H. Pitcock, D. Mokshagundam, M.H. Baik and S.J. Lippard, Direct nitric oxide detection in aqueous solution by copper(II) fluorescein complexes, Journal of the American Chemical Society 128(44) (2006), 14364-14373. (Pubitemid 44707746)
42. Y. Liu, A Comparative Study on Feature Selection Methods for Drug Discovery, J Chem Inf Model 44(5) (2004), 1823-1828.
43. R.L. Lord, H.J.Wang, M. Vieweger andM.H. Baik,What difference one double bond makes: Electronic structure of saturated and unsaturated n-heterocyclic carbene ligands in Grubbs 2nd generation-type catalysts, Journal of Organometallic Chemistry 691(24-25) (2006), 5505-5512. (Pubitemid 44791372)
44. Y.C. Martin, What Works and What Does Not: Lessons From Experience in a Pharmaceutical Company, QSAR & Combinatorial Science 25(12) (2006), 1192-1200. (Pubitemid 46052456)
45. A. Miller, Subset Selection in Regression, Chapman & Hall/CRC: Boca Raton, FL, 2002.
46. P.D. Mosier, A.E. Counterman, P.C. Jurs and D.E. Clemmer, Prediction of Peptide Ion Collision Cross Sections from Topological Molecular Structure and Amino Acid Parameters, Anal Chem 74 (2002), 1460-1370.
47. P.Murray-Rust, H.S. Rzepa, M.J.Williamson and E.L.Willighagen, Chemical markup, XML, and theWorldWideWeb. 5. Applications of Chemical Metadata in RSS Aggregators, J Chem Inf Comput Sci 44(2) (2004), 462-469.
48. S. Myung, M. Fioroni, R.R. Julian, S.L. Koeniger, M.H. Baik and D.E. Clemmer, Chirally directed formation of nanometer-scale proline clusters, Journal of the American Chemical Society 128(33) (2006), 10833-10839. (Pubitemid 44277771)
49. S. Myung, K.P. Lorton, S.I. Merenbloom, M. Fioroni, S.L. Koeniger, R.R. Julian, M.H. Baik and D.E. Clemmer, Evidence for spontaneous resolution of icosahedral proline, Journal of the American Chemical Society 128(50) (2006), 15988-15989. (Pubitemid 44936563)
50. T.I. Netzeva, A.P. Worth, T. Aldenberg, R. Benigni, M.T.D. Cronin, P. Gramatica, J.S. Jaworska, S. Kahn, G. Klopman, C.A.Marchant, G.Myatt, N. Nikolova-Jeliazkova, G.Y. Patlewicz, R. Perkins, D.W. Roberts, T.W. Schultz, D.T. Stanton, J.J.M. van de Sandt, W. Tong, G. Veith and C. Yang, Current Status of Methods for Defining the Applicability Domain of (Quantitative) Structure-Activity Relationships. The Report and Recommendations of ECVAMWorkshop 52, ATALA 33 (2005), 155-173. (Pubitemid 40686385)
51. O. Spjuth, T. Helmus, E.L. Willighagen, S. Kuhn, M. Eklund, J. Wagener, P. Murray-Rust, C. Steinbeck and J.E.S. Wikberg, Bioclipse: An Open Source Workbench for Chemo- and Bioinformatics, BMC Bioinformatics 8 (2007), 59.
52. D.T. Stanton, On The Physical Interpretation of QSAR Models, J Chem Inf Comput Sci 43(5) (2003), 1423-1433.
53. C. Steinbeck, C. Hoppe, S. Kuhn, M. Floris, R. Guha and E.L. Willighagen, Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics, Curr Pharm Des 12 (2006), 2110-2120.
54. R.D.C. Team, A Language and Environmnet for Statistical Computing, Foundation for Statistical Computing: Vienna, Austria, 2006.
55. A. Mauri, V. Consonni, M. Pavan and R. Todeschini, DRAGON software: An easy approach to molecular descriptor calculations, MATCH 56 (2006), 237-248.
56. H.J. Verhaar, J. SolbÈ, J. Speksnijder, C.J. van Leeuwen and J.L. Hermens, Classifying Environmental Pollutants: Part 3. External Validation of the Classification System, Chemosphere 40(8) (2000), 875-883. (Pubitemid 30094125)
57. J.D. Walker, I. Gerner, E. Hulzebos and K. Shlegel, The Skin Irritation Corrosion Rules Estimation Tool (SICRET), QSAR Comb Sci 24 (2005), 378-384. (Pubitemid 40637939)
58. D.J. Wild, Strategies for Using Information Effectively in Early-Stage Drug Discovery, in: Computer Applications in Pharmaceutical Research and Development, S. Ekins, ed., John Wiley & Sons: Hoboken, NJ, 2006, pp. 229-246.
59. D.J. Wild and G.D. Wiggins, Challenges for Chemoinformatics Education in Drug Discovery, Drug Discovery Today 11(9/10) (2006), 436-439.
60. D.J.Wild andG.D.Wiggins,Videoconferencing andOther Distance Education Techniques inChemoinformatics Teaching and Research at Indiana University, Journal of Chemical Information and Modeling 46(2) (2006), 495-502.
61. D.R. Williams, J.T. Reeves, P.P. Nag, W.H. Pitcock and M.H. Baik, Studies of the generation and pericyclic behavior of cyclic pentadienyl carbanions. Alkylation reactions as an efficient route to functionalized cis-bicyclo[3.3.0]octenes, Journal of the American Chemical Society 128(37) (2006), 12339-12348. (Pubitemid 44413864)
62. X. Yang and M.H. Baik, cis,cis-[(bpy)(2)(RuO)-O-V](2)O4+ catalyzes water oxidation formally via in situ generation of radicaloid Ru-IV-O center dot, Journal of the American Chemical Society 128(23) (2006), 7476-7485. (Pubitemid 43877520)
63. X. Zhang, K. Shedden and G.R. Rosania, A Cell-Based Molecular Transport Simulator for Pharmacokinetic Prediction and Cheminformatic Exploration, Molecular Pharmaceutics 3(6) (2006), 704-716. (Pubitemid 46087486)