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Journal Articles
- 2024
[j29]Jeremy Jones
, Robert D. Clark, Michael S. Lawless, David W. Miller, Marvin Waldman:
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations. J. Comput. Aided Mol. Des. 38(1): 14 (2024)- 2020
- [j28]Robert D. Clark, Denise N. Morris, Gary Chinigo, Michael S. Lawless, Jacques Prudhomme, Karine G. Le Roch, Maria José Lafuente, Santiago Ferrer, Francisco Javier Gamo, Robert Gadwood, Walter S. Woltosz:
Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones. J. Comput. Aided Mol. Des. 34(11): 1117-1132 (2020) - 2019
- [j27]Robert D. Clark:
A path to next-generation reproducibility in cheminformatics. J. Cheminformatics 11(1): 62:1-62:3 (2019) - 2015
- [j26]Marvin Waldman, Robert Fraczkiewicz, Robert D. Clark:
Tales from the war on error: the art and science of curating QSAR data. J. Comput. Aided Mol. Des. 29(9): 897-910 (2015) - [j25]Robert Fraczkiewicz, Mario Lobell, Andreas H. Göller, Ursula Krenz, Rolf Schoenneis, Robert D. Clark, Alexander Hillisch:
Best of Both Worlds: Combining Pharma Data and State of the Art Modeling Technology To Improve in Silico pKa Prediction. J. Chem. Inf. Model. 55(2): 389-397 (2015) - 2014
- [j24]Robert D. Clark, Wenkel Liang, Adam C. Lee, Michael S. Lawless, Robert Fraczkiewicz, Marvin Waldman:
Using beta binomials to estimate classification uncertainty for ensemble models. J. Cheminformatics 6(1): 34 (2014) - 2012
- [j23]Robert D. Clark, Marvin Waldman:
Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design. J. Comput. Aided Mol. Des. 26(1): 29-34 (2012) - 2009
- [j22]Robert D. Clark, Edmond J. Abrahamian:
Using a staged multi-objective optimization approach to find selective pharmacophore models. J. Comput. Aided Mol. Des. 23(11): 765-771 (2009) - [j21]Robert D. Clark:
DPRESS: Localizing estimates of predictive uncertainty. J. Cheminformatics 1: 11 (2009) - 2008
- [j20]Robert D. Clark, Daniel J. Webster-Clark:
Managing bias in ROC curves. J. Comput. Aided Mol. Des. 22(3-4): 141-146 (2008) - [j19]Robert D. Clark:
Preface to the special issue in memory of Phil Magee. J. Comput. Aided Mol. Des. 22(6-7): 333 (2008) - [j18]Robert D. Clark:
A ligand's-eye view of protein binding. J. Comput. Aided Mol. Des. 22(6-7): 507-521 (2008) - [j17]Roman J. Dorfman, Karl M. Smith, Brian B. Masek, Robert D. Clark:
A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. J. Comput. Aided Mol. Des. 22(9): 681-691 (2008) - [j16]R. Webster Homer, Jon Swanson, Robert J. Jilek, Tad Hurst, Robert D. Clark:
SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries. J. Chem. Inf. Model. 48(12): 2294-2307 (2008) - [j15]Peter C. Fox, Philippa R. N. Wolohan, Edmond J. Abrahamian, Robert D. Clark:
Parameterization and Conformational Sampling Effects in Pharmacophore Multiplet Searching. J. Chem. Inf. Model. 48(12): 2326-2334 (2008) - 2006
- [j14]Farhad Soltanshahi, Tamsin E. Mansley, Sun Choi, Robert D. Clark:
Balancing focused combinatorial libraries based on multiple GPCR ligands. J. Comput. Aided Mol. Des. 20(7-8): 529-538 (2006) - [j13]Nicola J. Richmond, Charlene A. Abrams, Philippa R. N. Wolohan, Edmond J. Abrahamian, Peter Willett, Robert D. Clark:
GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D. J. Comput. Aided Mol. Des. 20(9): 567-587 (2006) - [j12]Jennifer K. Shepphird, Robert D. Clark:
A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches. J. Comput. Aided Mol. Des. 20(12): 763-771 (2006) - [j11]Philippa R. N. Wolohan, Lakshmi B. Akella, Roman J. Dorfman, Peter G. Nell, Stefan M. Mundt, Robert D. Clark:
Structural Unit Analysis Identifies Lead Series and Facilitates Scaffold Hopping in Combinatorial Chemistry. J. Chem. Inf. Model. 46(3): 1188-1193 (2006) - [j10]Alex Strizhev, Edmond J. Abrahamian, Sun Choi, Joseph M. Leonard, Philippa R. N. Wolohan, Robert D. Clark:
The Effects of Biasing Torsional Mutations in a Conformational GA. J. Chem. Inf. Model. 46(4): 1862-1870 (2006) - 2004
- [j9]Robert D. Clark, Peter C. Fox:
Statistical variation in progressive scrambling. J. Comput. Aided Mol. Des. 18(7): 563-576 (2004) - 2003
- [j8]Philippa R. N. Wolohan, Robert D. Clark:
Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA. J. Comput. Aided Mol. Des. 17(1): 65-76 (2003) - [j7]Robert D. Clark:
Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics. J. Comput. Aided Mol. Des. 17(2-4): 265-275 (2003) - [j6]Edmond J. Abrahamian, Peter C. Fox, Lars Nærum, Inge Thøger Christensen, Henning Thøgersen, Robert D. Clark:
Efficient Generation, Storage, and Manipulation of Fully Flexible Pharmacophore Multiplets and Their Use in 3-D Similarity Searching. J. Chem. Inf. Comput. Sci. 43(2): 458-468 (2003) - [j5]Robert D. Clark, Julia Kar, Lakshmi B. Akella, Farhad Soltanshahi:
OptDesign: Extending Optimizable k-Dissimilarity Selection to Combinatorial Library Design. J. Chem. Inf. Comput. Sci. 43(3): 829-836 (2003) - [j4]Li Xing, Robert C. Glen, Robert D. Clark:
Predicting pKa by Molecular Tree Structured Fingerprints and PLS. J. Chem. Inf. Comput. Sci. 43(3): 870-879 (2003) - 1998
- [j3]Richard D. Cramer, David E. Patterson, Robert D. Clark, Farhad Soltanshahi, Michael S. Lawless:
Virtual Compound Libraries: A New Approach to Decision Making in Molecular Discovery Research. J. Chem. Inf. Comput. Sci. 38(6): 1010-1023 (1998) - [j2]Robert D. Clark, William J. Langton:
Balancing Representativeness Against Diversity using Optimizable K-Dissimilarity and Hierarchical Clustering. J. Chem. Inf. Comput. Sci. 38(6): 1079-1086 (1998) - 1997
- [j1]Robert D. Clark:
OptiSim: An Extended Dissimilarity Selection Method for Finding Diverse Representative Subsets. J. Chem. Inf. Comput. Sci. 37(6): 1181-1188 (1997)
Conference and Workshop Papers
- 2019
- [c1]Sergey Serebryakov, Dejan S. Milojicic, Natalia Vassilieva, Stephen Fleischman, Robert D. Clark:
Deep Learning Cookbook: Recipes for your AI Infrastructure and Applications. ICRC 2019: 16-24
Coauthor Index
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