Rachel Kolodny

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Approximate protein structural alignment in polynomial time
    Rachel Kolodny
    Departments of Computer Science and Structural Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:12201-6. 2004
  2. pmc Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
    Rachel Kolodny
    Department of Structural Biology, Fairchild Building, Stanford University, Stanford CA 94305, USA
    J Mol Biol 346:1173-88. 2005
  3. ncbi request reprint Small libraries of protein fragments model native protein structures accurately
    Rachel Kolodny
    Department of Structural Biology, Stanford University Medical School, Fairchild Building, Stanford, CA 94305, USA
    J Mol Biol 323:297-307. 2002
  4. ncbi request reprint VISTAL--a new 2D visualization tool of protein 3D structural alignments
    Rachel Kolodny
    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, Room 815, New York, NY 10032, USA
    Bioinformatics 22:2166-7. 2006
  5. ncbi request reprint Using an alignment of fragment strings for comparing protein structures
    Iddo Friedberg
    Program in Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
    Bioinformatics 23:e219-24. 2007
  6. ncbi request reprint Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction
    Rachel Kolodny
    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, Room 815, New York, NY 10032, USA
    Curr Opin Struct Biol 16:393-8. 2006
  7. ncbi request reprint Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons
    Yonatan Bilu
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    IEEE/ACM Trans Comput Biol Bioinform 3:408-22. 2006
  8. pmc Sequence-similar, structure-dissimilar protein pairs in the PDB
    Mickey Kosloff
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
    Proteins 71:891-902. 2008

Detail Information

Publications8

  1. pmc Approximate protein structural alignment in polynomial time
    Rachel Kolodny
    Departments of Computer Science and Structural Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:12201-6. 2004
    ..These insights can be used in the design of scoring functions for which the optimum can be approximated efficiently and perhaps in the development of efficient algorithms for the multiple structural alignment problem...
  2. pmc Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
    Rachel Kolodny
    Department of Structural Biology, Fairchild Building, Stanford University, Stanford CA 94305, USA
    J Mol Biol 346:1173-88. 2005
    ..This will have significant biological implications now that structural comparison has come to play a central role in the analysis of experimental work on protein structure, protein function and protein evolution...
  3. ncbi request reprint Small libraries of protein fragments model native protein structures accurately
    Rachel Kolodny
    Department of Structural Biology, Stanford University Medical School, Fairchild Building, Stanford, CA 94305, USA
    J Mol Biol 323:297-307. 2002
    ....
  4. ncbi request reprint VISTAL--a new 2D visualization tool of protein 3D structural alignments
    Rachel Kolodny
    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, Room 815, New York, NY 10032, USA
    Bioinformatics 22:2166-7. 2006
    ..AVAILABILITY: VISTAL can be downloaded from http://trantor.bioc.columbia.edu/~kolodny/software.html...
  5. ncbi request reprint Using an alignment of fragment strings for comparing protein structures
    Iddo Friedberg
    Program in Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
    Bioinformatics 23:e219-24. 2007
    ..However, in order to do so, there is a need to first understand how much information is contained in various possible 1D representations of protein structure...
  6. ncbi request reprint Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction
    Rachel Kolodny
    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, Room 815, New York, NY 10032, USA
    Curr Opin Struct Biol 16:393-8. 2006
    ..Significant relationships have been observed between proteins that belong to what have been termed different 'folds'. There has been progress in the use of these relationships in the prediction of protein structure and function...
  7. ncbi request reprint Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons
    Yonatan Bilu
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    IEEE/ACM Trans Comput Biol Bioinform 3:408-22. 2006
    ..Under the additional assumption that matches between segments are transitive, we further improve the running time for finding the optimal solution by restricting the search space of the dynamic programming algorithm...
  8. pmc Sequence-similar, structure-dissimilar protein pairs in the PDB
    Mickey Kosloff
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
    Proteins 71:891-902. 2008
    ..We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm)...