R D Clark

Summary

Affiliation: Tripos Inc
Country: USA

Publications

  1. ncbi Visualizing substructural fingerprints
    R D Clark
    Tripos Inc, 1699 South Hanley Avenue, St Louis, MO 63144, USA
    J Mol Graph Model 18:404-11, 527-32. 2000
  2. ncbi A ligand's-eye view of protein binding
    Robert D Clark
    Tripos Informatics Research Center, 1699 South Hanley Road, Saint Louis, MO, 63144, USA
    J Comput Aided Mol Des 22:507-21. 2008
  3. ncbi Managing bias in ROC curves
    Robert D Clark
    Tripos Informatics Research Center, 1699 South Hanley Road, Saint Louis, MO 63144, USA
    J Comput Aided Mol Des 22:141-6. 2008
  4. ncbi Modelling in vitro hepatotoxicity using molecular interaction fields and SIMCA
    Robert D Clark
    Tripos Inc, 1699 South Hanley Road, St Louis, MO 63144, USA
    J Mol Graph Model 22:487-97. 2004
  5. ncbi Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics
    Robert D Clark
    Tripos, Inc, 1699 S Hanley Road, St Louis, MO 63144, USA
    J Comput Aided Mol Des 17:265-75. 2003
  6. ncbi Preface to the special issue in memory of Phil Magee
    Robert D Clark
    Tripos International, 1699 S. Hanley Rd, St. Louis, MO, 63144, USA
    J Comput Aided Mol Des 22:333. 2008
  7. ncbi Molecular design and bioavailability
    Robert D Clark
    Tripos, Inc, St Louis, MO 63144, USA
    Curr Top Med Chem 3:1269-88. 2003
  8. ncbi Consensus scoring for ligand/protein interactions
    Robert D Clark
    Tripos Inc, St Louis, MO 63144, USA
    J Mol Graph Model 20:281-95. 2002
  9. ncbi Statistical variation in progressive scrambling
    Robert D Clark
    Tripos, Inc, 1699 S Hanley Road, St Louis, MO 63144, USA
    J Comput Aided Mol Des 18:563-76. 2004
  10. ncbi Using a staged multi-objective optimization approach to find selective pharmacophore models
    Robert D Clark
    Tripos International, Saint Louis, MO 63144, USA
    J Comput Aided Mol Des 23:765-71. 2009

Collaborators

Detail Information

Publications24

  1. ncbi Visualizing substructural fingerprints
    R D Clark
    Tripos Inc, 1699 South Hanley Avenue, St Louis, MO 63144, USA
    J Mol Graph Model 18:404-11, 527-32. 2000
    ..The nonlinear maps so obtained are useful for characterizing combinatorial libraries, for comparing sublibraries, and for exploring the distribution of biological properties across structural space...
  2. ncbi A ligand's-eye view of protein binding
    Robert D Clark
    Tripos Informatics Research Center, 1699 South Hanley Road, Saint Louis, MO, 63144, USA
    J Comput Aided Mol Des 22:507-21. 2008
    ....
  3. ncbi Managing bias in ROC curves
    Robert D Clark
    Tripos Informatics Research Center, 1699 South Hanley Road, Saint Louis, MO 63144, USA
    J Comput Aided Mol Des 22:141-6. 2008
    ..Either scheme is able to distinguish biased from unbiased screening statistics, but the harmonically weighted AUC in particular emphasizes the ability to place representatives of each class of active early in the recovery curve...
  4. ncbi Modelling in vitro hepatotoxicity using molecular interaction fields and SIMCA
    Robert D Clark
    Tripos Inc, 1699 South Hanley Road, St Louis, MO 63144, USA
    J Mol Graph Model 22:487-97. 2004
    ....
  5. ncbi Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics
    Robert D Clark
    Tripos, Inc, 1699 S Hanley Road, St Louis, MO 63144, USA
    J Comput Aided Mol Des 17:265-75. 2003
    ..The countervailing effects of training and test set size, diversity, and representativeness on PLS model statistics are described for CoMFA analysis of a large data set of COX2 inhibitors...
  6. ncbi Preface to the special issue in memory of Phil Magee
    Robert D Clark
    Tripos International, 1699 S. Hanley Rd, St. Louis, MO, 63144, USA
    J Comput Aided Mol Des 22:333. 2008
  7. ncbi Molecular design and bioavailability
    Robert D Clark
    Tripos, Inc, St Louis, MO 63144, USA
    Curr Top Med Chem 3:1269-88. 2003
    ..Papers discussing predictions pertaining to one or another aspect of bioavailability are also discussed, and some thoughts on future directions of work on in silico prediction in this area are presented...
  8. ncbi Consensus scoring for ligand/protein interactions
    Robert D Clark
    Tripos Inc, St Louis, MO 63144, USA
    J Mol Graph Model 20:281-95. 2002
    ..We find that the reliability and interpretability of results can be improved by combining results from all four functions into a CScore...
  9. ncbi Statistical variation in progressive scrambling
    Robert D Clark
    Tripos, Inc, 1699 S Hanley Road, St Louis, MO 63144, USA
    J Comput Aided Mol Des 18:563-76. 2004
    ..It is shown that the three statistics are all robust for stable PLS models, in terms of the stochastic component of their determination and of their variation due to sampling effects involved in training set selection...
  10. ncbi Using a staged multi-objective optimization approach to find selective pharmacophore models
    Robert D Clark
    Tripos International, Saint Louis, MO 63144, USA
    J Comput Aided Mol Des 23:765-71. 2009
    ..This makes GALAHAD a potentially powerful tool for identifying discriminating models, as is illustrated here using a set of dopaminergic agonists that vary in their D1 vs. D2 receptor selectivity...
  11. ncbi Parameterization and conformational sampling effects in pharmacophore multiplet searching
    Peter C Fox
    Tripos International, 1699 South Hanley Road, St Louis, Missouri 63144, USA
    J Chem Inf Model 48:2326-34. 2008
    ..Consolidating information from multiple known actives or establishing single "bioactive" conformations a priori are safer ways to improve discrimination in pharmacophoric multiplet searching...
  12. ncbi A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches
    Jennifer K Shepphird
    Informatics Research Center, Tripos Inc, 1699 South Hanley Road, St. Louis, MO 63144, USA
    J Comput Aided Mol Des 20:763-71. 2006
    ..1-1% of decoy databases. The differences in discriminating power ranged from 2 to 20-fold, depending on the protein target and the type of pharmacophore multiplet used...
  13. ncbi Prospective ligand- and target-based 3D QSAR: state of the art 2008
    Robert D Clark
    Biochemical Infometrics, St Louis, MO 63141, USA
    Curr Top Med Chem 9:791-810. 2009
    ....
  14. ncbi "Lead hopping". Validation of topomer similarity as a superior predictor of similar biological activities
    Richard D Cramer
    Tripos Discovery Research, Bude Stratton Business Park, Bude, Cornwall EX23 8LY, UK
    J Med Chem 47:6777-91. 2004
    ..Conversely, the least similar 75% of structures contained 0.3% actives for topomer similarity vs 1.0% actives for Tanimoto 2D fingerprint similarity, a 3-fold superiority for topomers in avoiding false negatives...
  15. ncbi Predicting pK(a) by molecular tree structured fingerprints and PLS
    Li Xing
    Tripos, Inc, 1699 S Hanley Road, St Louis, Missouri 63144, USA
    J Chem Inf Comput Sci 43:870-9. 2003
    ..41 for acids and 0.30 for bases) and yielded accurate predictions on an external test set. The quality and statistical performance of pK(a) prediction has been improved considerably over the initial implementation of the method...
  16. ncbi OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space
    Dennis G Sprous
    Tripos Inc, 1699 South Hanley Road, St. Louis, Missouri 63144, USA
    J Comb Chem 6:530-9. 2004
    ..As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches...
  17. ncbi Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA
    Philippa R N Wolohan
    Tripos, Inc, 1699 South Hanley Road, Saint Louis, Missouri 63144, USA
    J Comput Aided Mol Des 17:65-76. 2003
    ....
  18. ncbi Efficient generation, storage, and manipulation of fully flexible pharmacophore multiplets and their use in 3-D similarity searching
    Edmond Abrahamian
    Tripos, Inc, 1699 South Hanley Road, St. Louis, Missouri 63144, USA
    J Chem Inf Comput Sci 43:458-68. 2003
    ..Its use frees the user from having to ensure strict comparability of starting conformations and having to use fixed torsional increments, thereby allowing fully flexible characterization of pharmacophoric patterns...
  19. ncbi A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
    Roman J Dorfman
    Tripos Informatics Research Center, 1699 S Hanley Road, St Louis, MO, 63144, USA
    J Comput Aided Mol Des 22:681-91. 2008
    ..They are also quantitatively compared with a broader range of techniques in terms of speed and the ability to reproduce bound ligand conformations found in complexes with proteins...
  20. ncbi Structural unit analysis identifies lead series and facilitates scaffold hopping in combinatorial chemistry
    Philippa R N Wolohan
    Tripos, Inc, 1699 S. Hanley Road, St. Louis, Missouri 63144, USA
    J Chem Inf Model 46:1188-93. 2006
    ..SUA was able to successfully identify promising alternative core structures in addition to identifying compounds with above-average activity and selectivity...
  21. ncbi Balancing focused combinatorial libraries based on multiple GPCR ligands
    Farhad Soltanshahi
    Informatics Research Center, Tripos, Inc, 1699 S. Hanley Road, St Louis, MO 63144, USA
    J Comput Aided Mol Des 20:529-38. 2006
    ..A novel pivoting technique is described which makes it possible to generate promising designs even under those circumstances. The approach is illustrated by application to some serotonergic agonists and chemokine antagonists...
  22. ncbi The effects of biasing torsional mutations in a conformational GA
    Alex Strizhev
    Tripos, Inc, 1699 South Hanley Road, St. Louis, Missouri 63144, USA
    J Chem Inf Model 46:1862-70. 2006
    ..Overall, torsionally biased sampling produces good models comprised of energetically favorable ligand conformations...
  23. ncbi GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D
    Nicola J Richmond
    Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, 211 Portobello St, Sheffield, S7 4DP, UK
    J Comput Aided Mol Des 20:567-87. 2006
    ....
  24. ncbi Alignment of three-dimensional molecules using an image recognition algorithm
    Nicola J Richmond
    Department of Information Studies, Krebs Institute for Biomolecular Research, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
    J Mol Graph Model 23:199-209. 2004
    ..A range of examples is provided to demonstrate the efficiency and effectiveness of the method...