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Journal Article
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
Moll M, Bryant DH, Kavraki LE.  2010.  The LabelHash Algorithm for Substructure Matching. BMC Bioinformatics. 11(1):555.
Abstract      Preprint PDF     Publisher's web site     
Moll M, Bryant DH, Kavraki LE.  2011.  The LabelHash Server and Tools for Substructure-Based Functional Annotation. Bioinformatics. 27:2161--2162.
Abstract      Preprint PDF     Publisher's web site     
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     
Haspel N, Geisbrecht B, Lambris JD, Kavraki LE.  2009.  Multi-scale Characterization of the Energy Landscape of Proteins with Application to the C3d/Efb-C Complex. Proteins: Structure, function and bioinformatics. 78:1004-1014.
     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     
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     
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
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, Kavraki LE.  2008.  LabelHash: A Flexible and Extensible Method for Matching Structural Motifs. Automated Function Prediction / BioSapiens meeting (AFP-BioSapiens).
Preprint PDF     Publisher's web site     
Moll M, Kavraki LE.  2008.  Matching of Structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction. The Seventh Annual International Conference on Computational Systems Bioinformatics (CSB2008). :157-168.
Abstract      Preprint PDF     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