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Conference Paper
Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE.  2005.  Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. Pacific Symposium on Biocomputing.
Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.  2006.  Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction. Systems Bioinformatics Conference (CSB). 4:311-323.
Abstract           Publisher's web site     
Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kimmel M, Lichtarge O, Kavraki LE.  2007.  Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction. Computational Systems Bioinformatics Conference (CSB2007). :343-355.
Abstract      Preprint PDF
LaValle S, Finn PW, Kavraki LE, Latombe J-C.  1999.  Efficient Database Screening for Rational Drug Design Using Pharmacophore-Constrained Conformational Search. The Third ACM International Conference on Computational Biology (RECOMB). :250-259.
Preprint PDF     Publisher's web site     
Finn PW, Halperin D, Kavraki LE, Latombe J-C, Motwani R, Shelton C, Venkat S.  1996.  Geometric Manipulation of Flexible Ligands. LNCS Series Applied Computational Geometry - Towards Geometric Engineering. 1148:67-78.
Preprint PDF     Publisher's web site     
Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE.  2006.  Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. Research in Computational Biology: 10th Annual International Conference (RECOMB).
Abstract           Publisher's web site     
Moll M, Goldberg KY, Erdmann MA, Fearing RS.  2002.  Orienting Micro-Scale Parts with Squeeze and Roll Primitives. Proc. 2002 IEEE Intl. Conf. on Robotics and Automation. :1931--1936.
Abstract      Preprint PDF     Publisher's web site     
Haeberlen A, Flannery E, Ladd AM, Rudys A, Wallach DS, Kavraki LE.  2004.  Practical Robust Localization over Large-Scale 802.11 Wireless Networks. Proceedings of the Tenth ACM International Conference on Mobile Computing and Networking (MOBICOM 2004). :70-84.
Abstract      Preprint PDF     Publisher's web site     
Finn PW, Kavraki LE, Latombe J-C, Motwani R, Shelton C, Venkatasubramanian S, Yao A.  1997.  RAPID: Randomized Pharmacophore Identification for drug design. ACM Conference on Computational Geometry. :324-333.
Abstract      Preprint PDF     Publisher's web site     
Finn PW, Kavraki LE, Latombe J-C, Motwani R, Venkatasubramanian S.  1997.  Search Techniques for Rational Drug Design. International Conference on Intelligent Information Systems. :2-6.
Abstract           Publisher's web site     
Fofanov VY, Chen BY, Bryant DH, Moll M, Lichtarge O, Kavraki LE, Kimmel M.  2008.  A Statistical Model to Correct Systematic Bias Introduced by Algorithmic Thresholds in Protein Structural Comparison Algorithms. IEEE Intl. Conf. on Bioinformatics and Biomedicine (BIBM).
Abstract      Preprint PDF     Publisher's web site     
Journal Article
Moll M, Goldberg KY, Erdmann MA, Fearing RS.  2002.  Aligning Parts for Micro Assemblies. Assembly Automation. 22:46--54.
Abstract      Preprint PDF     Publisher's web site     
Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE.  2010.  Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics. 11:242.
Abstract      Preprint PDF     Publisher's web site     
Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.  2007.  Cavity Scaling: Automated Refinement of Cavity-Aware Motifs in Protein Function Prediction. Journal of Bioinformatics and Computational Biology. 5:353-382.
Abstract      Preprint PDF
Finn PW, Kavraki LE.  1999.  Computational Approaches to Drug Design. Algorithmica. 25:347-371.
Preprint PDF
Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE.  2007.  The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. Journal of Computational Biology. 14:791-816.
Abstract      Preprint PDF     Publisher's web site     
Kristensen DM, Ward MR, Lisewski AM, Edrin S, Chen BY, Fofanov VY, Kimmel M, Lichtarge O.  2008.  Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics. 9(17)
Abstract           Publisher's web site     
LaValle S, Finn PW, Kavraki LE, Latombe J-C.  2000.  A Randomized Kinematics-based Approach to Pharmacophore-Constrained Conformational Search and Database Screening. Journal of Computational Chemistry. 21:731-747.
Abstract      Preprint PDF
Finn PW, Kavraki LE, Latombe J-C, Shelton C, Venkatasubramanian S, Yao A.  1998.  RAPID: Randomized Pharmacophore Identification for drug design. Computational Geometry: Theory and Applications. 10(4):263-272.
Abstract      Preprint PDF     Publisher's web site     
Kristensen DM, Chen BY, Fofanov VY, Ward MR, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O.  2006.  Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity. Protein Science. 15:1530-1536.
     Publisher's web site