Krzysztof Ginalski

Summary

Affiliation: University of Texas Southwestern Medical Center
Country: USA

Publications

  1. ncbi request reprint BOF: a novel family of bacterial OB-fold proteins
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    FEBS Lett 567:297-301. 2004
  2. ncbi request reprint Raptor protein contains a caspase-like domain
    Krzysztof Ginalski
    Biochemistry Department, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Trends Biochem Sci 29:522-4. 2004
  3. ncbi request reprint BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Trends Biochem Sci 29:392-5. 2004
  4. ncbi request reprint DCC proteins: a novel family of thiol-disulfide oxidoreductases
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Trends Biochem Sci 29:339-42. 2004
  5. pmc Protein structure prediction for the male-specific region of the human Y chromosome
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Proc Natl Acad Sci U S A 101:2305-10. 2004
  6. pmc A comprehensive update of the sequence and structure classification of kinases
    Sara Cheek
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
    BMC Struct Biol 5:6. 2005
  7. pmc Identification of novel restriction endonuclease-like fold families among hypothetical proteins
    Lisa N Kinch
    Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 33:3598-605. 2005
  8. pmc Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade
    Lisa N Kinch
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Protein Sci 15:84-93. 2006
  9. ncbi request reprint SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family
    Alexander Dikiy
    Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
    Biochemistry 46:6871-82. 2007
  10. pmc Detecting distant homology with Meta-BASIC
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Nucleic Acids Res 32:W576-81. 2004

Collaborators

Detail Information

Publications40

  1. ncbi request reprint BOF: a novel family of bacterial OB-fold proteins
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    FEBS Lett 567:297-301. 2004
    ....
  2. ncbi request reprint Raptor protein contains a caspase-like domain
    Krzysztof Ginalski
    Biochemistry Department, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Trends Biochem Sci 29:522-4. 2004
    ..This finding suggests several unexpected aspects of raptor function in the target of rapamycin (TOR) signaling pathway...
  3. ncbi request reprint BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Trends Biochem Sci 29:392-5. 2004
    ..Inspection of neighboring genes encoding BTLCPs suggests a link between this predicted activity and a type-I secretion system resembling ATP-binding cassette exporters of toxins and proteases involved in bacterial pathogenicity...
  4. ncbi request reprint DCC proteins: a novel family of thiol-disulfide oxidoreductases
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Trends Biochem Sci 29:339-42. 2004
  5. pmc Protein structure prediction for the male-specific region of the human Y chromosome
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9038, USA
    Proc Natl Acad Sci U S A 101:2305-10. 2004
    ..The data presented here set up the basis for additional scientific discoveries in human biology of the Y chromosome, which plays a fundamental role in sex determination...
  6. pmc A comprehensive update of the sequence and structure classification of kinases
    Sara Cheek
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, USA
    BMC Struct Biol 5:6. 2005
    ..This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme...
  7. pmc Identification of novel restriction endonuclease-like fold families among hypothetical proteins
    Lisa N Kinch
    Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9050, USA
    Nucleic Acids Res 33:3598-605. 2005
    ..Finally, our method identifies a novel restriction endonuclease-like domain in the C-terminus of RecC that is not detected with structure-based searches of the existing PDB database...
  8. pmc Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade
    Lisa N Kinch
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390 9050, USA
    Protein Sci 15:84-93. 2006
    ..Finally, conserved genomic neighborhoods of S2P homologs allow functional predictions for PDZ-containing transmembrane proteases in extra-cytoplasmic stress response and lipid metabolism...
  9. ncbi request reprint SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family
    Alexander Dikiy
    Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
    Biochemistry 46:6871-82. 2007
    ..Rdx12 was found to interact with glutathione peroxidase 1, whereas 14-3-3 protein was identified as one of the targets of mammalian SelW, suggesting a mechanism for redox regulation of the 14-3-3 family of proteins...
  10. pmc Detecting distant homology with Meta-BASIC
    Krzysztof Ginalski
    Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
    Nucleic Acids Res 32:W576-81. 2004
    ..pl. Detailed discussion is provided for two of the most interesting assignments. DUF271 and DUF431 are predicted to be a nucleotide-diphospho-sugar transferase and an alpha/beta-knot SAM-dependent RNA methyltransferase, respectively...
  11. ncbi request reprint Protein domain of unknown function DUF1023 is an alpha/beta hydrolase
    Mingzhu Zheng
    Department of Biochemistry, University of Texas, Southwestern Medical Center, Dallas, Texas 75390 9038, USA
    Proteins 59:1-6. 2005
    ..We predict DUF1023 spatial structure and deduce that they function as hydrolases utilizing catalytic Ser-His-Asp triad with the serine as a nucleophile...
  12. pmc Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity
    Tim A Rand
    Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Proc Natl Acad Sci U S A 101:14385-9. 2004
    ....
  13. pmc PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
    Marcin von Grotthuss
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    BMC Bioinformatics 7:53. 2006
    ..Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity...
  14. ncbi request reprint Prediction of signal peptides in protein sequences by neural networks
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warszawa, Poland
    Acta Biochim Pol 55:261-7. 2008
    ..As a consequence, the method can be easily applied to genome-wide datasets. The software can be downloaded freely from http://rpsp.bioinfo.pl/RPSP.tar.gz...
  15. pmc Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease
    Lukasz Knizewski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Poland
    J Virol 80:2575-7. 2006
    ....
  16. ncbi request reprint Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases
    Lukasz Knizewski
    Cell Cycle 7:542-4. 2008
  17. ncbi request reprint AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5A, 02 106, Warsaw, Poland
    J Mol Model 14:69-76. 2008
    ..bioinfo.pl/ . Additionally, the reference dataset for optimization of prediction of phosphorylation sites, collected from the UniProtKB was also provided and can be accessed at http://ams2.bioinfo.pl/data/ ...
  18. ncbi request reprint Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding
    Lukasz Knizewski
    Cell Cycle 6:1666-70. 2007
  19. pmc Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches
    Lukasz Knizewski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, Warsaw, Poland
    BMC Struct Biol 7:40. 2007
    ....
  20. ncbi request reprint Comparative modeling for protein structure prediction
    Krzysztof Ginalski
    Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, 02 106 Warsaw, Poland
    Curr Opin Struct Biol 16:172-7. 2006
    ..For difficult targets, for which the most significant progress in recent years has been observed, optimal template selection and alignment accuracy are still the major problems...
  21. ncbi request reprint In silico prediction of SARS protease inhibitors by virtual high throughput screening
    Dariusz Plewczynski
    Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Pawinskiego 5a Street, 02 106 Warsaw, Poland
    Chem Biol Drug Des 69:269-79. 2007
    ..Selected molecules having close structural relationship to a 2-methyl-2,4-pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors...
  22. ncbi request reprint Bacillus subtilis YkuK protein is distantly related to RNase H
    Łukasz Knizewski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, 02 106 Warsaw, Poland
    FEMS Microbiol Lett 251:341-6. 2005
    ....
  23. ncbi request reprint Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III
    Masood Z Hadi
    Molecular and Structural Biology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    J Mol Biol 316:853-66. 2002
    ....
  24. ncbi request reprint 3D-Jury: a simple approach to improve protein structure predictions
    Krzysztof Ginalski
    BioInfoBank Institute, Limanowskiego 24A, 60 744 Poznan, Poland
    Bioinformatics 19:1015-8. 2003
    ..PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)..
  25. pmc Detection of reliable and unexpected protein fold predictions using 3D-Jury
    Krzysztof Ginalski
    Bioinformatics Laboratory, BioInfoBank Institute, ul Limanowskiego 24A, 60 744 Poznan, Poland
    Nucleic Acids Res 31:3291-2. 2003
    ..This can point to interesting relationships which could have been missed in annotations of proteins or genomes and provide very valuable information for novel scientific discoveries...
  26. pmc ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure
    Krzysztof Ginalski
    Bioinformatics Laboratory, BioInfoBank Institute, ul Limanowskiego 24A, 60 744 Poznan, Poland
    Nucleic Acids Res 31:3804-7. 2003
    ..The specificity of the alignment score is improved in the lower specificity range compared with the robust sequence-only profiles...
  27. ncbi request reprint Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
    Krzysztof Ginalski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland
    Proteins 53:410-7. 2003
    ....
  28. ncbi request reprint Application of 3D-Jury, GRDB, and Verify3D in fold recognition
    Marcin von Grotthuss
    BioInfoBank Institute, Poznan, Poland
    Proteins 53:418-23. 2003
    ....
  29. ncbi request reprint ECEPE proteins: a novel family of eukaryotic cysteine proteinases
    Krzysztof Ginalski
    Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, 02 106 Warsaw, Poland
    Trends Biochem Sci 29:524-6. 2004
    ..The presence of the invariant Cys-His-Asp/Asn catalytic triad and the oxyanion-hole glutamine residue characteristic of papain-like cysteine proteases indicate that ECEPE proteins might function as proteases...
  30. pmc Practical lessons from protein structure prediction
    Krzysztof Ginalski
    BioInfoBank Institute ul Limanowskiego 24A, 60 744 Poznan, Poland
    Nucleic Acids Res 33:1874-91. 2005
    ..This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed...
  31. pmc Sequence-structure mapping errors in the PDB: OB-fold domains
    Ceslovas Venclovas
    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, L 448, PO Box 808, Livermore, CA 94551, USA
    Protein Sci 13:1594-602. 2004
    ..Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions...
  32. ncbi request reprint Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses
    Peter Borowski
    Abteilung fur Virologie, Bernhard Nocht Institut fur Tropenmedizin, Hamburg, Germany
    Eur J Biochem 270:1645-53. 2003
    ..The halogeno benzimidazoles and benzotriazoles included in this study are excellent lead compounds for the development of more potent inhibitors of hepatitis C virus and other viral NTPase/helicases...
  33. ncbi request reprint HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein
    Lucjan S Wyrwicz
    Cell Cycle 7:269-71. 2008
  34. doi request reprint Mitochondrial release factor in yeast: interplay of functional domains
    Jan Kutner
    Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02 106, Warsaw, Poland
    Curr Genet 53:185-92. 2008
    ..This explains how the suppressor mutants may facilitate translation termination despite a defect in decoding of the stop signal...
  35. ncbi request reprint Novel SARS unique AdoMet-dependent methyltransferase
    Krzysztof Ginalski
    Cell Cycle 5:2414-6. 2006
  36. ncbi request reprint Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution
    Gye Won Han
    Joint Center for Structural Genomics, La Jolla, CA 92037, USA
    Proteins 64:1083-90. 2006
  37. ncbi request reprint DUF1613 is a novel family of eucaryotic AdoMet-dependent methyltransferases
    Lukasz Knizewski
    Cell Cycle 5:1580-2. 2006
  38. ncbi request reprint Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes
    Joanna Towpik
    Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02 106 Warsaw, Poland
    J Biol Chem 279:14096-103. 2004
    ....
  39. ncbi request reprint Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily
    Kamil Steczkiewicz
    Cell Cycle 5:2927-30. 2006
  40. pmc Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440
    Jose I Jiménez
    Departments of Molecular Microbiology and Protein Science, Centro de Investigaciones Biologicas Consejo Superior de Investigaciones Cientificas, 28040 Madrid, Spain
    Proc Natl Acad Sci U S A 105:11329-34. 2008
    ....