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Algorithms & Applications Group
Computational Biology
Protein Folding
Ligand Binding
RNA Folding
Neuron PRM
Decoy Databases

Here are our projects. Click on the sliding image to learn more.

Motion planning, as its name suggests, plans a path (motion) for a movable object. Even though it originated in, and has mainly been applied to, robotics problems, motion planning as a concept is abstract enough to be applied to any motion related application, ranging from robotics to animation, and most recently to computational biology, chemistry and neuroscience. Our group is investigating applications of probabilistic roadmap (PRM) motion planning methods to protein folding, ligand binding (i.e., drug docking, which arises in drug design), RNA folding, neuroscience, and decoy databases. We also have a Protein Folding Server available where you can submit your proteins for analysis by our motion planning technique.

Papers

Protein Folding

Adaptive Local Learning in Sampling Based Motion Planning for Protein Folding, Chinwe Ekenna, Shawna Thomas, Nancy Amato, Bio Med Central Systems Biology, 10(2):165--179, Aug 2016. Also, In The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 61-68, Washington DC, USA, Nov 2015.
Journal(pdf, abstract) Proceedings(pdf, abstract)

Improved Sampling Based Motion Planning Through Local Learning, Chinwe Ekenna, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Aug 2016.
Ph.D. Thesis(pdf, abstract)

Adaptive Neighbor Connection Aids Protein Motion Modeling, Chinwe Ekenna, Shawna Thomas, Nancy Amato, In Proc. RSS Workshop on Robotics Methods for Structural and Dynamic Modeling of Molecular Systems, Jul 2014.
Proceedings(ps, pdf, abstract)

Rigidity Analysis for Protein Motion and Folding Core Identification, Shawna Thomas, Lydia Tapia, Chinwe Ekenna, Hsin-Yi (Cindy) Yeh, Nancy M. Amato, In Proc. of 2013 AAAI Wkshp. on Art. Int. and Robot. Meth. in Comp. Bio., Bellevue, WA, Jul 2013.
Proceedings(pdf, abstract)

A Multi-Directional Rapidly Exploring Random Graph (mRRG) for Protein Folding, Shuvra Nath, Shawna Thomas, Chinwe Ekenna, Nancy M. Amato, In ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 44-51, Orlando, FL, USA, Oct 2012.
Proceedings(ps, pdf, abstract)

A Motion Planning Approach to Studying Molecular Motions, Lydia Tapia, Shawna Thomas, Nancy M. Amato, Communications in Information and Systems, 10(1):53-68, 2010.
Journal(pdf, abstract)

Rigidity Analysis for Modeling Protein Motion, Shawna Thomas, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, May 2010.
Ph.D. Thesis(ps, pdf, abstract)

Intelligent Motion Planning and Analysis with Probabilistic Roadmap Methods for the Study of Complex and High-Dimensional Motions, Lydia Tapia, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, Dec 2009.
Ph.D. Thesis(pdf, abstract)

Using Dimensionality Reduction to Better Capture RNA and Protein Folding Motions, Lydia Tapia, Shawna Thomas, Nancy M. Amato, Technical Report, TR08-005, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, U.S.A., Oct 2008.
Technical Report(ps, pdf, abstract)

Techniques for Modeling and Analyzing RNA and Protein Folding Energy Landscapes, Xinyu Tang, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2007.
Ph.D. Thesis(ps, pdf, abstract)

Kinetics Analysis Methods For Approximate Folding Landscapes, Lydia Tapia, Xinyu Tang, Shawna Thomas, Nancy M. Amato, In Int. Conf. on Int. Sys. for Mol. Bio. (ISMB)/European Conf. on Comp. Bio.(ECCB), Vienna, Austria, Jul 2007. Also, Bioinformatics, 23(13):i539-i548, Jul 2007.
Journal(pdf, abstract)

Simulating Protein Motions with Rigidity Analysis, Shawna Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato, Journal of Computational Biology, 14(6):839-855, Jul 2007. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 394-409, Apr 2006.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract)

Parallel Protein Folding with STAPL, Shawna Thomas, Gabriel Tanase, Lucia K. Dale, Jose M. Moreira, Lawrence Rauchwerger, Nancy M. Amato, Concurrency and Computation: Practice and Experience, 17(14):1643-1656, Dec 2005.
Journal(ps, pdf, abstract)

Protein Folding by Motion Planning, Shawna Thomas, Guang Song, Nancy M. Amato, Physical Biology, 2:S148-S155, Nov 2005.
Journal(ps, pdf, abstract)

Parallel Protein Folding with STAPL, Shawna Thomas, Nancy M. Amato, In Proc. IEEE Int. Wkshp. on High Performance Computational Biology, Santa Fe, NM, Apr 2004.
Proceedings(ps, pdf, abstract)

A Motion Planning Approach to Folding: From Paper Craft to Protein Folding, Guang Song, Nancy M. Amato, IEEE Transactions on Robotics and Automation, 20(1):60-71, Feb 2004. Also, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 948-953, Seoul, Korea, May 2001. Also, Technical Report, TR00-017, Department of Computer Science and Engineering, Texas A&M University, Jul 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

A Motion Planning Approach to Protein Folding, Guang Song, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, Dec 2003.
Ph.D. Thesis(ps, abstract)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Nancy M. Amato, Ken Dill, Guang Song, Journal of Computational Biology, 10(3-4):239-255, Jun 2003. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 2-11, Apr 2002.
Journal(ps, pdf, abstract) Proceedings(pdf, abstract)

A Path Planning-based Study of Protein Folding With a Case Study of Hairpin Formation in Protein G and L, Guang Song, Shawna Thomas, Ken A. Dill, J. Martin Scholtz, Nancy M. Amato, In Proc. Pac. Symp. of Biocomputing (PSB), pp. 240-251, Lihue, HI, Jan 2003.
Proceedings(ps, pdf, abstract)

Using Motion Planning to Study Protein Folding Pathways, Guang Song, Nancy M. Amato, Journal of Computational Biology, 9(2):149-168, Nov 2002. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 287-296, Apr 2001. Also, Technical Report, TR00-026, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2000.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Nancy M. Amato, Guang Song, Technical Report, TR01-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Technical Report(ps, pdf, abstract)

A Motion Planning Approach to Folding: From Paper Craft to Protein Structure Prediction, Guang Song, Nancy M. Amato, Technical Report, TR00-001, Department of Computer Science and Engineering, Texas A&M University, Jan 2000.
Technical Report(ps)

Probabilistic Roadmap Methods are Embarrassingly Parallel, Nancy M. Amato, Lucia K. Dale, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 688-694, Detroit, Michigan, USA, May 1999.
Proceedings(ps, pdf, abstract)

Ligand Binding

Using Motion Planning to Evaluate Protein Binding Site Accessibility, Diane Uwacu, Everett Yang, Shawna Thomas, Nancy M. Amato, Technical Report, TR18-001, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station TX 77848, USA, Jul 2018.
Technical Report(pdf, abstract)

Uniform Sampling Framework for Sampling Based Motion Planning and Its Applications to Robotics and Protein Ligand Binding, Hsin-Yi (Cindy) Yeh, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, May 2016.
Ph.D. Thesis(pdf, abstract)

Solving Motion Planning Problems by Iterative Relaxation of Constraints, Osman BurÁhan Bayazit, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, U.S.A., May 2003.
Ph.D. Thesis(ps, pdf, abstract)

Ligand Binding with OBPRM and Haptic User Input, O. Burchan Bayazit, Guang Song, Nancy M. Amato, In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pp. 954-959, May 2001.
Proceedings(ps, pdf, abstract)

Ligand Binding with OBPRM and Haptic User Input: Enhancing Automatic Motion Planning with Virtual Touch, O. Burchan Bayazit, Guang Song, Nancy M. Amato, Technical Report, TR00-025, Department of Computer Science and Engineering, Texas A&M University, Oct 2000.
Technical Report(ps, pdf, abstract)

RNA Folding

A Motion Planning Approach to Studying Molecular Motions, Lydia Tapia, Shawna Thomas, Nancy M. Amato, Communications in Information and Systems, 10(1):53-68, 2010.
Journal(pdf, abstract)

Intelligent Motion Planning and Analysis with Probabilistic Roadmap Methods for the Study of Complex and High-Dimensional Motions, Lydia Tapia, Ph.D. Thesis, Parasol Laboratory, Department of Computer Science, Texas A&M University, College Station, Texas, Dec 2009.
Ph.D. Thesis(pdf, abstract)

Simulating RNA Folding Kinetics on Approximated Energy Landscapes, Xinyu Tang, Shawna Thomas, Lydia Tapia, David P. Giedroc, Nancy M. Amato, Journal of Molecular Biology, 3811(4):1055-1067, Sep 2008.
Journal(pdf, abstract)

Techniques for Modeling and Analyzing RNA and Protein Folding Energy Landscapes, Xinyu Tang, Ph.D. Thesis, Department of Computer Science and Engineering, Texas A&M University, Dec 2007.
Ph.D. Thesis(ps, pdf, abstract)

Tools for Simulating and Analyzing RNA Folding Kinetics, Xinyu Tang, Shawna Thomas, Lydia Tapia, Nancy M. Amato, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 268-282, San Francisco, CA, Apr 2007.
Proceedings(ps, pdf, abstract)

Using Motion Planning to Study RNA Folding Kinetics, Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato, Journal of Computational Biology, 12(6):862-881, Jul 2005. Also, In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pp. 252-261, San Diego, CA, Mar 2004.
Journal(ps, pdf, abstract) Proceedings(ps, pdf, abstract)

Neuron PRM

Neuron PRM: A Framework for Constructing Cortical Networks, Jyh-Ming Lien, Marco Morales, Nancy M. Amato, Neurocomputing, 52-54(28):191-197, Jun 2003. Also, Technical Report, TR01-002, Parasol Laboratory, Department of Computer Science, Texas A&M University, Oct 2001.
Journal(ps, pdf, abstract) Technical Report(ps, pdf, abstract)

Decoy Databases

Decoy Database Improvement for Protein Folding, Hsin-Yi (Cindy) Yeh, Aaron Lindsey, Chih-Peng Wu, Shawna Thomas, Nancy M. Amato, Journal of Computational Biology, 22(9):823 - 836, Sep 2015.
Journal(pdf, abstract)

Improving Decoy Databases for Protein Folding Algorithms, Aaron Lindsey, Hsin-Yi (Cindy) Yeh, Chih-Peng Wu, Shawna Thomas, Nancy M. Amato, In ACM Conf. on Bioinformatics, Comput. Biology and Health Informatics on Computational Structural Bioinformatics Wkshp., pp. 717 - 724, Newport Beach, CA, Sep 2014.
Proceedings(ps, pdf, abstract)

Improving Decoy Databases for Protein Folding Algorithms , Aaron Lindsey, Hsin-Yi (Cindy) Yeh, Chih-Peng Wu, Shawna Thomas, Nancy M. Amato, In Proc.of 2014 RSS Wkshp. on Robotics Methods for Structural and Dynamic Modeling of Molecular Systems, Berkeley, CA, Jul 2014.
Proceedings(ps, pdf, abstract)


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