Research Topics
Genomes and Genes | Krzysztof GinalskiSummaryAffiliation: University of Texas Southwestern Medical Center Country: USA Publications
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Publications
BOF: a novel family of bacterial OB-fold proteinsKrzysztof 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....- Raptor protein contains a caspase-like domainKrzysztof 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... - BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinasesKrzysztof 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... - DCC proteins: a novel family of thiol-disulfide oxidoreductasesKrzysztof 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 
Protein structure prediction for the male-specific region of the human Y chromosomeKrzysztof 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...
A comprehensive update of the sequence and structure classification of kinasesSara 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...- Identification of novel restriction endonuclease-like fold families among hypothetical proteinsLisa 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... - Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascadeLisa 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... - SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like familyAlexander 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... - Detecting distant homology with Meta-BASICKrzysztof 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... - Protein domain of unknown function DUF1023 is an alpha/beta hydrolaseMingzhu 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... - Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activityTim 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.... - PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomicsMarcin 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... - Prediction of signal peptides in protein sequences by neural networksDariusz 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... - Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonucleaseLukasz Knizewski
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Poland
J Virol 80:2575-7. 2006.... - Uncharacterized DUF1574 leptospira proteins are SGNH hydrolasesLukasz Knizewski
Cell Cycle 7:542-4. 2008 - AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 updateDariusz 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/ ... - Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA bindingLukasz Knizewski
Cell Cycle 6:1666-70. 2007 - Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searchesLukasz Knizewski
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, Warsaw, Poland
BMC Struct Biol 7:40. 2007.... - Comparative modeling for protein structure predictionKrzysztof 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... - In silico prediction of SARS protease inhibitors by virtual high throughput screeningDariusz 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... - Bacillus subtilis YkuK protein is distantly related to RNase HŁukasz Knizewski
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5A, 02 106 Warsaw, Poland
FEMS Microbiol Lett 251:341-6. 2005.... - Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease IIIMasood Z Hadi
Molecular and Structural Biology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
J Mol Biol 316:853-66. 2002.... - 3D-Jury: a simple approach to improve protein structure predictionsKrzysztof 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/).. - Detection of reliable and unexpected protein fold predictions using 3D-JuryKrzysztof 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... - ORFeus: Detection of distant homology using sequence profiles and predicted secondary structureKrzysztof 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... - Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessmentKrzysztof Ginalski
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland
Proteins 53:410-7. 2003.... - Application of 3D-Jury, GRDB, and Verify3D in fold recognitionMarcin von Grotthuss
BioInfoBank Institute, Poznan, Poland
Proteins 53:418-23. 2003.... - ECEPE proteins: a novel family of eukaryotic cysteine proteinasesKrzysztof 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... - Practical lessons from protein structure predictionKrzysztof Ginalski
BioInfoBank Institute ul. Limanowskiego 24A, 60-744 Pozna, 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... - Sequence-structure mapping errors in the PDB: OB-fold domainsCeslovas 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... - Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related virusesPeter 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... - HSV-1 UL45 encodes a carbohydrate binding C-type lectin proteinLucjan S Wyrwicz
Cell Cycle 7:269-71. 2008 
Mitochondrial release factor in yeast: interplay of functional domainsJan 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...- Novel SARS unique AdoMet-dependent methyltransferaseKrzysztof Ginalski
Cell Cycle 5:2414-6. 2006 - Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolutionGye Won Han
Joint Center for Structural Genomics, La Jolla, CA 92037, USA
Proteins 64:1083-90. 2006 - DUF1613 is a novel family of eucaryotic AdoMet-dependent methyltransferasesLukasz Knizewski
Cell Cycle 5:1580-2. 2006 - Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomesJoanna Towpik
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02 106 Warsaw, Poland
J Biol Chem 279:14096-103. 2004.... - Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamilyKamil Steczkiewicz
Cell Cycle 5:2927-30. 2006 - Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440Jose 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....