Research Topics
| S Sri KrishnaSummaryAffiliation: University of Texas Southwestern Medical Center Country: USA Publications
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Detail Information
Publications
A tale of two ferredoxins: sequence similarity and structural differencesS 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...- Representing and comparing protein structures as paths in three-dimensional spaceDegui 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... - Structural classification of zinc fingers: survey and summaryS 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... 
The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbonS 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...- Structural classification of small, disulfide-rich protein domainsSara 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... - 4SCOPmap: automated assignment of protein structures to evolutionary superfamiliesSara 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... - CASP5 assessment of fold recognition target predictionsLisa 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... - PALSSE: a program to delineate linear secondary structural elements from protein structuresIndraneel 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... - Structural drift: a possible path to protein fold changeS 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..contact: ... - Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active siteMichael DiDonato
The Joint Center for Structural Genomics
Proteins 65:771-6. 2006 - Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolutionQingping Xu
The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA
Proteins 64:808-13. 2006 - Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle foldPiotr Kozbial
Joint Center for Structural Genomics, La Jolla, California, USA
Proteins 71:1589-96. 2008 - Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) foldKevin Kai Jin
The Joint Center for Structural Genomics, Menlo Park, California, USA
Proteins 63:1112-8. 2006 - Structurally analogous proteins do exist!S Sri Krishna
Structure 12:1125-7. 2004 - Influence of a mutation in the ATP-binding region of Ca2+/calmodulin-dependent protein kinase II on its interaction with peptide substratesMullasseril 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... - Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolutionQingping Xu
Joint Center for Structural Genomics, Menlo Park, California, USA
Proteins 71:1546-52. 2008 - Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolutionHerbert 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 - Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolutionChloe Zubieta
Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA
Proteins 68:999-1005. 2007 - Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolutionMickey 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... - Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1pQingping Xu
Joint Center for Structural Genomics
Proteins 65:777-82. 2006 - Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 A resolutionMichael DiDonato
Joint Center for Structural Genomics, USA
Proteins 63:256-60. 2006 - Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new foldRobert Schwarzenbacher
Joint Center for Structural Genomics
Proteins 65:243-8. 2006 - Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolutionIrimpan I Mathews
Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA
Proteins 63:1106-11. 2006 - A zinc-binding dual-specificity YVH1 phosphatase in the malaria parasite, Plasmodium falciparum, and its interaction with the nuclear protein, pescadilloRajinder 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...