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2020 – today
- 2022
[j36]Qinfang Sun, Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson, Andres Emanuelli Castaner, Karen Kirby, Stefan G. Sarafianos, Nan-Jie Deng
, Ronald M. Levy:
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J. Comput. Aided Mol. Des. 36(3): 193-203 (2022)- 2021
- [j35]Adam Gardner, Ludovic Autin, Daniel Fuentes, Martina Maritan, Benjamin A. Barad, Michaela Medina, Arthur J. Olson, Danielle A. Grotjahn, David S. Goodsell:
CellPAINT: Turnkey Illustration of Molecular Cell Biology. Frontiers Bioinform. 1 (2021) - 2020
- [c12]Ludovic Autin, Martina Maritan, Brett A. Barbaro, Adam Gardner, Arthur J. Olson, Michel F. Sanner, David S. Goodsell:
Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation. MolVa@Eurographics/EuroVis 2020: 23-31
2010 – 2019
- 2019
- [j34]Nicholas Waldin, Manuela Waldner, Mathieu Le Muzic, M. Eduard Gröller, David S. Goodsell, Ludovic Autin, Arthur J. Olson, Ivan Viola:
Cuttlefish: Color Mapping for Dynamic Multi-Scale Visualizations. Comput. Graph. Forum 38(6): 150-164 (2019) - [j33]Tobias Klein, Peter Mindek, Ludovic Autin, David S. Goodsell, Arthur J. Olson, M. Eduard Gröller, Ivan Viola:
Parallel Generation and Visualization of Bacterial Genome Structures. Comput. Graph. Forum 38(7): 57-68 (2019) - [j32]Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy:
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. J. Chem. Inf. Model. 59(4): 1382-1397 (2019) - [j31]David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli:
Integrative modeling of the HIV-1 ribonucleoprotein complex. PLoS Comput. Biol. 15(6) (2019) - [j30]David Kouril, Ladislav Cmolík, Barbora Kozlíková, Hsiang-Yun Wu, Graham Johnson, David S. Goodsell, Arthur J. Olson, M. Eduard Gröller, Ivan Viola:
Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments. IEEE Trans. Vis. Comput. Graph. 25(1): 977-986 (2019) - 2018
- [j29]Adam Gardner, Ludovic Autin, Brett Barbaro, Arthur J. Olson, David S. Goodsell:
CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments. IEEE Computer Graphics and Applications 38(6): 51-66 (2018) - [j28]Tobias Klein, Ludovic Autin, Barbora Kozlíková, David S. Goodsell, Arthur J. Olson, M. Eduard Gröller, Ivan Viola:
Instant Construction and Visualization of Crowded Biological Environments. IEEE Trans. Vis. Comput. Graph. 24(1): 862-872 (2018) - 2016
- [j27]Richard K. Belew, Stefano Forli, David S. Goodsell, T. J. O'Donnell, Arthur J. Olson:
Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives. J. Chem. Inf. Model. 56(8): 1597-1607 (2016) - 2015
- [j26]Alexander L. Perryman, Weixuan Yu, Xin Wang, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge, Arthur J. Olson:
A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA. J. Chem. Inf. Model. 55(3): 645-659 (2015) - [j25]Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner:
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Comput. Biol. 11(12) (2015) - 2014
- [j24]Raghu Machiraju, Carsten Görg, Arthur J. Olson:
Visual Analytics for Biological Data. IEEE Computer Graphics and Applications 34(2): 24-25 (2014) - [j23]David L. Mobley, Shuai Liu, Nathan M. Lim, Karisa L. Wymer, Alexander L. Perryman, Stefano Forli, Nan-Jie Deng, Justin Su, Kim Branson, Arthur J. Olson:
Blind prediction of HIV integrase binding from the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28(4): 327-345 (2014) - [j22]Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson:
Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. J. Comput. Aided Mol. Des. 28(4): 429-441 (2014) - [j21]Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy:
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28(4): 475-490 (2014) - [j20]Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson:
AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. J. Chem. Inf. Model. 54(8): 2371-2379 (2014) - [c11]Jodi L. Davenport, Matt Silberglitt, Jon Boxerman, Arthur J. Olson:
Identifying Affordances of 3D Printed Tangible Models for Understanding Core Biological Concepts. ICLS 2014 - 2013
- [j19]Garrett M. Morris, Luke G. Green, Zoran Radic, Palmer Taylor, K. Barry Sharpless, Arthur J. Olson, Flavio Grynszpan:
Automated Docking with Protein Flexibility in the Design of Femtomolar "Click Chemistry" Inhibitors of Acetylcholinesterase. J. Chem. Inf. Model. 53(4): 898-906 (2013) - 2012
- [j18]Siripit Pitchuanchom, Chantana Boonyarat, Stefano Forli, Arthur J. Olson, Chavi Yenjai:
Cyclin-dependent kinases 5 template: Useful for virtual screening. Comput. Biol. Medicine 42(1): 106-111 (2012) - [j17]Ludovic Autin, Graham Johnson, Johan Hake, Arthur J. Olson, Michel F. Sanner:
uPy: A Ubiquitous CG Python API with Biological-Modeling Applications. IEEE Computer Graphics and Applications 32(5): 50-61 (2012) - [j16]Sandro Cosconati, Luciana Marinelli, Francesco Saverio Di Leva, Valeria La Pietra, Angela De Simone, Francesca Mancini, Vincenza Andrisano, Ettore Novellino, David S. Goodsell, Arthur J. Olson:
Protein Flexibility in Virtual Screening: The BACE-1 Case Study. J. Chem. Inf. Model. 52(10): 2697-2704 (2012) - 2011
- [j15]Jui-Chih Wang, Jung-Hsin Lin, Chung-Ming Chen, Alex L. Perryman, Arthur J. Olson:
Robust Scoring Functions for Protein-Ligand Interactions with Quantum Chemical Charge Models. J. Chem. Inf. Model. 51(10): 2528-2537 (2011) - 2010
- [j14]Oleg Trott, Arthur J. Olson:
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31(2): 455-461 (2010)
2000 – 2009
- 2009
- [j13]Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson:
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30(16): 2785-2791 (2009) - 2008
- [j12]Max W. Chang, Richard K. Belew, Kate S. Carroll, Arthur J. Olson, David S. Goodsell:
Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes. J. Comput. Chem. 29(11): 1753-1761 (2008) - 2007
- [j11]Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell:
A semiempirical free energy force field with charge-based desolvation. J. Comput. Chem. 28(6): 1145-1152 (2007) - [j10]Max W. Chang, William Lindstrom, Arthur J. Olson, Richard K. Belew:
Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries. J. Chem. Inf. Model. 47(3): 1258-1262 (2007) - 2005
- [j9]Alexandre Gillet, Michel F. Sanner, Daniel Stoffler, Arthur J. Olson:
Tangible Augmented Interfaces for Structural Molecular Biology. IEEE Computer Graphics and Applications 25(2): 13-17 (2005) - 2004
- [c10]Alexandre Gillet, Suzanne Weghorst, William Winn, Daniel Stoffler, Michel F. Sanner, David S. Goodsell, Arthur J. Olson:
Computer-linked autofabricated 3D models for teaching structural biology. SIGGRAPH Sketches 2004: 28 - [c9]Alexandre Gillet, Michel F. Sanner, Daniel Stoffler, David S. Goodsell, Arthur J. Olson:
Augmented Reality with Tangible Auto-Fabricated Models for Molecular Biology Applications. IEEE Visualization 2004: 235-242 - 2003
- [j8]Robin J. Rosenfeld, David S. Goodsell, Rabi A. Musah, Garrett M. Morris, David B. Goodin, Arthur J. Olson:
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. J. Comput. Aided Mol. Des. 17(8): 525-536 (2003) - [c8]Ganesh Sankaranarayanan, Suzanne Weghorst, Michel F. Sanner, Alexandre Gillet, Arthur J. Olson:
Role of Haptics in Teaching Structural Molecular Biolog. HAPTICS 2003: 363-366 - [c7]Daniel Stoffler, Sophie I. Coon, Ruth Huey, Arthur J. Olson, Michel F. Sanner:
Integrating Biomolecular Analysis and Visual Programming: Flexibility and Interactivity in the Design of Bioinformatics Tools. HICSS 2003: 275 - 2002
- [c6]Ikuko Takanashi, Eric B. Lum, Kwan-Liu Ma, Jörg Meyer, Bernd Hamann, Arthur J. Olson:
Segmentation and 3D visualization of high-resolution human brain cryosections. Visualization and Data Analysis 2002: 55-61
1990 – 1999
- 1999
- [c5]Michel F. Sanner, Bruce S. Duncan, C. J. Carrillo, Arthur J. Olson:
Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS. Pacific Symposium on Biocomputing 1999: 401-412 - 1998
- [j7]Christopher D. Rosin, Richard K. Belew, Garrett M. Morris, Arthur J. Olson, David S. Goodsell:
Computational Coevolution of Antiviral Drug Resistance. Artif. Life 4(1): 41-59 (1998) - [j6]Garrett M. Morris, David S. Goodsell, Robert S. Halliday, Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson:
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19(14): 1639-1662 (1998) - 1996
- [j5]Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson:
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J. Comput. Aided Mol. Des. 10(4): 293-304 (1996) - [j4]Boris A. Reva, Michel F. Sanner, Arthur J. Olson, Alexei V. Finkelstein:
Lattice modeling: Accuracy of energy calculations. J. Comput. Chem. 17(8): 1025-1032 (1996) - [c4]Bruce S. Duncan, Arthur J. Olson:
Applications of Evolutionary Programming for the Prediction of Protein-Protein Interactions. Evolutionary Programming 1996: 411-417 - 1995
- [j3]Boris A. Reva, Dmitrii S. Rykunov, Arthur J. Olson, Alexei V. Finkelstein:
Constructing Lattice Models of Protein Chains with Side Groups. J. Comput. Biol. 2(4): 527-535 (1995) - [c3]Michel F. Sanner, Arthur J. Olson, Jean-Claude Spehner:
Fast and Robust Computation of Molecular Surfaces. SCG 1995: C6-C7
1980 – 1989
- 1989
- [c2]David S. Goodsell, Arthur J. Olson:
Molecular applications of volume rendering and 3-D texture maps. VVS 1989: 27-31 - 1985
- [j2]Michael L. Connolly, Arthur J. Olson:
GRANNY, a companion to GRAMPS for the real-time manipulation of macromolecular models. Comput. Chem. 9(1): 1-6 (1985) - 1983
- [j1]Richard A. Alden, Gerard Bricogne, Stephan T. Freer, Sid R. Hall, Wayne A. Hendrickson, Penelope Anne Machin, Robert J. Munn, Arthur J. Olson, George N. Reeke Jr.:
Cooperative programming in crich ystallography. Comput. Chem. 7(3): 137-148 (1983) - 1981
- [c1]T. J. O'Donnell, Arthur J. Olson:
GRAMPS - A graphics language interpreter for real-time, interactive, three-dimensional picture editing and animation. SIGGRAPH 1981: 133-142
Coauthor Index
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