Robotics Science and Systems

Berkeley, California, July 12, 2014

Full-day Workshop

Anticipated Schedule

Location: 206 Wheeler on the UC Berkeley Campus

8:00 - 9:00 am Morning Coffee and Poster Setup
9:00 - 9:05 am Welcome and Introductions

9:05 - 9:50 am Invited Talk: Configuration Spaces of Symmetry-Constrained Motions in Crystals
Greg Chirikjian
9:50 - 10:10 am Collision-Free Configuration-Spaces in Macromolecular Crystals
Gregory S. Chirikjian and Bernard Shiffman (Paper)
10:05 - 10:30 am Editing molecular structures with smoothed articulated-body accelerations
Stephane Redon (Paper)

10:30 - 11:00 am Coffee Break

11:00 - 11:20 am On the Stochastic Roadmap to Model Functionally-related Structural Transitions in Wildtype and Variant Proteins
Kevin Molloy, Rudy Clausen and Amarda Shehu (Paper)
11:20 - 11:40 pm Adaptive Neighbor Connection Aids Protein Motion Modeling
Chinwe Ekenna, Shawna Thomas and Nancy Amato (Paper)
11:40 - 12:00 pm An Efficient Method for Quantitative Delineation of How Protein Breathing Motions Open Ligand Migration Channels
Hyuntae Na and Guang Song (Paper)
12:00 - 12:20 pm Geometric Issues in Dimensionality Reduction and Protein Conformation Space
Mojie Duan, Li Han, Lee Rudolph and Shuanghong Huo (Paper)

12:20 - 14:00 pm Lunch Break (Group order and TVs for world cup match)

14:00 - 14:30 pm Invited Talk: Geometry and Robotics-inspired Methods for the Analysis of Protein Strcuture and Function
Lydia Kavraki
14:30 - 15:00 pm Motion Planning for Large Molecular Complexes
Mark Moll
15:00 - 15:15 pm Crowdsourced Molecular Docking Using Path-Planning and Haptic Devices
Torin Adamson, John Baxter, Kasra Manavi, Bruna Jacobson and Lydia Tapia (Paper)
15:15 - 15:20 pm Functional Annotation of Proteins Through Substructure Matching
Mark Moll, Drew H. Bryant, and Lydia E. Kavraki
(Poster Abstract)
15:20 - 15:25 pm Effect of Geometry and Bacterial Collisions on the Motion of Micro Bio Robots
Elizabeth Beattie, Edward Steager and Vijay Kumar
(Poster Abstract)

15:25 - 16:15 pm Coffee Break and Posters
Characterizing Synthetically Engineered Cells for Sensors in Micro Bio Robots
Denise Wong, Edward B. Steager and Vijay Kumar
(Poster Abstract)
Toward fully automated high performance computing drug discovery: A massively parallel virtual screening pipeline for docking and molecular mechanics/generalized born surface area rescoring to improve enrichment
Xiaohua Zhang, Sergio Wong and Felice Lightstone
(Poster Abstract)

16:15 - 16:35 pm Influence of Model Resolution on Antibody Aggregation Simulations
Kasra Manavi and Lydia Tapia (Paper)
16:35 - 16:55 pm Improving Decoy Databases for Protein Folding Algorithms
Aaron Lindsey, Hsin-Yi Yeh, Chih-Peng Wu, Shawna Thomas and Nancy Amato (Paper)
16:55 - 17:15 pm Towards De Novo Folding of Protein Structures from Cryo-EM 3D Images at Medium Resolutions
Jing He and Dong Si (Paper)

17:15 - ?? pm Discussion and Group Dinner