S Sri Krishna

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. pmc A tale of two ferredoxins: sequence similarity and structural differences
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Struct Biol 6:8. 2006
  2. pmc Representing and comparing protein structures as paths in three-dimensional space
    Degui Zhi
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    BMC Bioinformatics 7:460. 2006
  3. pmc Structural classification of zinc fingers: survey and summary
    S Sri Krishna
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 31:532-50. 2003
  4. ncbi request reprint The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon
    S Sri Krishna
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Cell Cycle 3:1046-9. 2004
  5. ncbi request reprint Structural classification of small, disulfide-rich protein domains
    Sara Cheek
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390, USA
    J Mol Biol 359:215-37. 2006
  6. pmc 4SCOPmap: automated assignment of protein structures to evolutionary superfamilies
    Sara Cheek
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
    BMC Bioinformatics 5:197. 2004
  7. ncbi request reprint CASP5 assessment of fold recognition target predictions
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Proteins 53:395-409. 2003
  8. pmc PALSSE: a program to delineate linear secondary structural elements from protein structures
    Indraneel Majumdar
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
    BMC Bioinformatics 6:202. 2005
  9. ncbi request reprint Structural drift: a possible path to protein fold change
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 21:1308-10. 2005
  10. ncbi request reprint Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site
    Michael DiDonato
    The Joint Center for Structural Genomics
    Proteins 65:771-6. 2006

Collaborators

Detail Information

Publications24

  1. pmc A tale of two ferredoxins: sequence similarity and structural differences
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    BMC Struct Biol 6:8. 2006
    ..Profile-based methods for sequence comparison, such as PSI-BLAST and HMMer, suggest statistically significant similarity between these domains...
  2. pmc Representing and comparing protein structures as paths in three-dimensional space
    Degui Zhi
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    BMC Bioinformatics 7:460. 2006
    ..Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction...
  3. pmc Structural classification of zinc fingers: survey and summary
    S Sri Krishna
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 31:532-50. 2003
    ..The classification helps in understanding the relationship between the structure, function and evolutionary history of these domains. The results are available as an online database of zinc finger structures...
  4. ncbi request reprint The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon
    S Sri Krishna
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Cell Cycle 3:1046-9. 2004
    ..By comparative sequence and structural analysis, we show that the previously uncharacterized finger domain insert to the catalytic core of HAUSP is a zinc ribbon that has lost its zinc-binding ability...
  5. ncbi request reprint Structural classification of small, disulfide-rich protein domains
    Sara Cheek
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390, USA
    J Mol Biol 359:215-37. 2006
    ..Examples of variations in disulfide bonding patterns found within families and fold groups are discussed...
  6. pmc 4SCOPmap: automated assignment of protein structures to evolutionary superfamilies
    Sara Cheek
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
    BMC Bioinformatics 5:197. 2004
    ..To address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the SCOP database...
  7. ncbi request reprint CASP5 assessment of fold recognition target predictions
    Lisa N Kinch
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9050, USA
    Proteins 53:395-409. 2003
    ..We also compared the results of manual groups to those of automatic servers evaluated in parallel by CAFASP, showing that the top performing automated server structure predictions approached those of the best manual predictors...
  8. pmc PALSSE: a program to delineate linear secondary structural elements from protein structures
    Indraneel Majumdar
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
    BMC Bioinformatics 6:202. 2005
    ..Success of such structural comparison methods depends crucially on the accurate identification and delineation of secondary structure elements...
  9. ncbi request reprint Structural drift: a possible path to protein fold change
    S Sri Krishna
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Bioinformatics 21:1308-10. 2005
    ....
  10. ncbi request reprint Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site
    Michael DiDonato
    The Joint Center for Structural Genomics
    Proteins 65:771-6. 2006
  11. ncbi request reprint Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution
    Qingping Xu
    The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA
    Proteins 64:808-13. 2006
  12. doi request reprint Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold
    Piotr Kozbial
    Joint Center for Structural Genomics, La Jolla, California, USA
    Proteins 71:1589-96. 2008
  13. ncbi request reprint Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold
    Kevin Kai Jin
    The Joint Center for Structural Genomics, Menlo Park, California, USA
    Proteins 63:1112-8. 2006
  14. ncbi request reprint Structurally analogous proteins do exist!
    S Sri Krishna
    Structure 12:1125-7. 2004
  15. pmc Influence of a mutation in the ATP-binding region of Ca2+/calmodulin-dependent protein kinase II on its interaction with peptide substrates
    Mullasseril Praseeda
    Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Thiruvananthapuram, Kerala 695014, India
    Biochem J 378:391-7. 2004
    ..Molecular modelling suggests structural changes are likely to occur at the peptide-binding pocket in the active state of the enzyme as a consequence of the Glu-60-->Gly mutation...
  16. doi request reprint Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution
    Qingping Xu
    Joint Center for Structural Genomics, Menlo Park, California, USA
    Proteins 71:1546-52. 2008
  17. doi request reprint Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution
    Herbert L Axelrod
    Joint Center for Structural Genomics JCSG, The Scripps Research Institute, BCC206, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proteins 71:1042-9. 2008
  18. ncbi request reprint Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution
    Chloe Zubieta
    Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA
    Proteins 68:999-1005. 2007
  19. ncbi request reprint Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution
    Mickey Kosloff
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
    Proteins 65:527-37. 2006
    ..Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies...
  20. ncbi request reprint Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p
    Qingping Xu
    Joint Center for Structural Genomics
    Proteins 65:777-82. 2006
  21. ncbi request reprint Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 A resolution
    Michael DiDonato
    Joint Center for Structural Genomics, USA
    Proteins 63:256-60. 2006
  22. ncbi request reprint Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold
    Robert Schwarzenbacher
    Joint Center for Structural Genomics
    Proteins 65:243-8. 2006
  23. ncbi request reprint Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution
    Irimpan I Mathews
    Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA
    Proteins 63:1106-11. 2006
  24. ncbi request reprint A zinc-binding dual-specificity YVH1 phosphatase in the malaria parasite, Plasmodium falciparum, and its interaction with the nuclear protein, pescadillo
    Rajinder Kumar
    Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, 307 University Boulevard, Mobile, AL 36688 0002, USA
    Mol Biochem Parasitol 133:297-310. 2004
    ..PfYVH1 represents the first dual-specificity zinc-finger phosphatase characterized in the protozoan kingdom...