Biblio

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2008
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     
2007
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
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     
2006
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, 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     
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     
2005
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.
2003
Yao H, Kristensen DM, Mihalek I, Sowa M, Shaw C, Kimmel M, Kavraki LE, Lichtarge O.  2003.  An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures. Journal of Molecular Biology. 326:255-261.
Abstract           Publisher's web site