Kevin Molloy's Publications

Journal Publications


  1. A. Estaña, K. Molloy, M. Vaisset, B. Sibille, T. Simeon, P. Bernado, J. Cortés. Hybrid parallelization of a multi-tree path search algorithm: Application to highly-flexible biomolecules. Parallel Computing, June 2018. [IF: 0.938]
  2. Kevin Molloy, Laurent Denarie, Marc Vaisset, Thierry Siméon, Juan Cortés. Simultaneous System Design and Path Planning: A sampling-based algorithm. International Journal of Robotics Research, July 2018. [IF: 2.503]
  3. Kevin Molloy, Amarda Shehu. A General, Adaptive, Roadmap-based Algorithm for Protein Motion Computation. IEEE Trans NanoBioScience 2015 (in press). [IF: 1.77]
  4. Didier Devaurs, Kevin Molloy, Marc Vaisset, Amarda Shehu, Thierry Siméon, and Juan Cortés. Characterizing Energy Landscapes of Peptides using a Combination of Stochastic Algorithms. IEEE Trans NanoBioScience , 2015, 14:545-552. [IF: 1.77]
  5. Kevin Molloy, Rudy Clausen, Amarda Shehu. A Stochastic Roadmap Method to Model Protein Structural Transitions. Robotica , December 2015. [IF: 0.894]
  6. Kevin Molloy, M. Jennifer Van, Daniel Barbará and Amarda Shehu. Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. BMC Bioinformatics, 15 (Suppl 8):S4, 2014. [IF: 3.02] [Citations: 2]
  7. Kevin Molloy, Sameh Saleh, and Amarda Shehu. Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab-initio Protein Structure Prediction. IEEE Transactions in Computational Biology and Bioinformatics, 1162-1175, 2013.(IF 2.25) [Citations: 8].
  8. Kevin Molloy and Amarda Shehu. Elucidating the Ensemble of Functionally-relevant Transitions in Protein Systems with a Robotics-inspired Method. BMC Structural Biology Journal, 13(Suppl 1):S8, 2013. [IF: 2.09] [Citations: 8]
  9. Brian Olson, Irina Hashmi, Kevin Molloy, and Amarda Shehu. Basin Hopping as a General and Versatile Optimization Framework for the Characterizations of Biological Macromolecules. Advances in Artificial Intelligence, 2012, 674832 (special issue on Artificial Intellegence in Biomedicine). [Citations:12]
  10. Brian Olson, Kevin Molloy, S-Farid Hendi, and Amarda Shehu. Guiding Search in the Protein Conformational Space with Structural Profiles>. Journal of Bioinformatics and Computational Biology, 2012, 10(3):1242005 (IF:1.063) [Citations:17].
  11. Brian Olson, Kevin Molloy, and Amarda Shehu. In Search of the Protein Native State with a Probabilistic Sampling Approach. Journal of Bioinformatics and Computational Biology, 9(3):383-398(IF: 1.063) [Citations:26].

Conference Publications


  1. Laurent Denarie, Kevin Molloy, Marc Vaisset, Thierry Siméon, and Juan Cortés. Combining System Design and Path Planning. To Appear at WAFR (Workshop on Algorithmic Foundations of Robotics), San Francisco, CA. 2016.
  2. Kevin Molloy and Amarda Shehu. Interleaving Global and Local Search for Protein Motion Computation. International Symposium on Bioinformatics Research and Applications (ISBRA), Norfolk, VA, June 2015.
  3. Kevin Molloy and Amarda Shehu. A Probabilistic Roadmap-based Method to Model Conformational Switching of a Protein Among Many Functionally-relevant Structures. 6th International Conf on Bioinformatics and Computational Biology (BiCOB), Las Vegas, NV, 2014 ( nalist for best paper award). [Citations: 1]
  4. Kevin Molloy, Jennifer M. Van, Daniel Barbará, and Amarda Shehu. Higher-order Representations for Automated Organization of Protein Structure Space. IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), New Orleans, LA, 2013
  5. Kevin Molloy and Amarda Shehu. A Robotics-inspired Method to Sample Conformational Paths Connecting Known Functionally-relevant Structures in Protein Systems. In Comput Struct Biol Workshop (CSBW), Philadelphia, PA, 2012.
  6. Kevin Molloy and Amarda Shehu. Biased Decoy Sampling to Identify Near-Native Protein Conformations. In ACM Bioinf. and Comp. Biology (BCB), Orlando, FL. 2012.
  7. Brian Olson, Kevin Molloy, and Amarda Shehu. "Enhancing Sampling of the Conformational Space Near the Protein Native State". Intl. Conference on Bio-inspired Models of Network, Information, and Computing Systems (BIONETICS), Boston, MA, 2010 (best student paper award).
  8. Kevin Molloy, Daniel Menasce. Method and Model to Assess the Performance of Clustered Databases: The Oracle RAC Case. 2010 Computer Measurement Group Conf., Orlando, FL, Dec6-8,2010.


Workshop Publications


  1. Kevin Molloy, Rudy Clausen, and Amarda Shehu. On the Stochastic Roadmap to Model Functionally-related Structural Transitions in Wildtype and Varient Proteins. Workshop on Robotic Methods for Structural and Dynamic Modeling of Molecular Systems, Berkeley, California, July 2014.
  2. Kevin Molloy, Amarda Shehu. A Robotics-inspired Method to Sample Conformational Paths Connecting Known Functionally-relevant Structures in Protein Systems. In Comput Struct Biol Workshop (CSBW), IEEE BIBM Workshops, Philadelphia, PA, 20112, pg. 56-63.

Book Chapters


  1. Amarda Shehu, Daniel Barbará, and Kevin Molloy. A Survey of Compuational Methods for Protein Function Prediction. In Big Analytics in Genomics (Springer), first edition (Editors:Wong, K.C.), 2016.

Talks


  1. Characterizing Energy Landscapes of Small Peptides. Atomic and Molecular Computation Workshop, University Paul Sabatier, Toulouse, France. November 2015.
  2. Probabilistic Algorithms for Studying Protein Structure and Dynamics. Robotics and Interactions research group. LAAS/CNRS, Toulouse, France, April 2015.
  3. Probabilistic Algorithms for Modeling Protein Structure and Dynamics. Computational Materials Science Center and the School of Physics, Astronomy, and Computational Sciences. George Mason University, Fairfax, VA. February 2015.
  4. Algorithmic Frameworks for Modeling Structures, Motions, and Assembly of Protein Molecules. Guest lecture for BENG 420 (bioinformatics for engineers), Volgenau School of Engineering (VSE), George Mason University, Fairfax, VA. October 2014.
  5. On the Stchastic Roadmap to Model Functionally-related Structural Transitions in Wildtype and Variant Proteins. RSS Workshop on Robotic Methods for Structural and Dynamic Modeling of Molecular Systems (RMMS), Berkeley, CA, USA, July 2014.
  6. Higher-order Representations for Automated Organization of Protein Structure Space. International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), New Orleans, LA. June 2013.
  7. A Robotics-inspired Method to Sample Conformational Paths Connecting Known Functionally-relevant Structures in Protein Systems. Computational Structure Biology Workshop (CSBW), Philadelphia, PA. Oct 2012.
  8. Biased Decoy Sampling to Identify Near-Native Protein Conformations. ACM Bioinformatics and Computational Biology Conference (BCB), Orlando, FL. Oct. 2012.
  9. Method and Model to Assess the Performance of Clustered Databases: The Oracle RAC Case. 2010 Computer Measurement Group Conference, December 9, 2010, Orlando, FL.