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Krzysztof Ginalski

Research Profile

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Genes & Molecular Sequences

Amino Acid Sequences

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Physiology

Protein Folding

Chemicals & Drugs

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Publications

TOP 3
Nicola Crosetto; Marzena Bienko; Roberto Chiarle; Norbert Dojer; Krzysztof Ginalski; Elif Karaca; Abhishek Mitra; Philippe Pasero; Maga Rowicka; Maria Joao Silva; Magdalena Skrzypczak; Qi Wang; Ivan Dikic
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.
Roman Szczesny; Lukasz S Borowski; Krzysztof Ginalski; Monika S Hejnowicz; Anna Muszewska; Kamil Steczkiewicz; Andrzej Dziembowski
Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.
Seweryn Mroczek; Iwo Kuciński; Krzysztof Ginalski; Joanna Krwawicz; Jan Kutner; Michal Lazniewski; Andrzej Dziembowski
C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification.

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All Publications

2013: Nicola Crosetto; Marzena Bienko; Roberto Chiarle; Norbert Dojer; Krzysztof Ginalski; Elif Karaca; Abhishek Mitra; Philippe Pasero; Maga Rowicka; Maria Joao Silva; Magdalena Skrzypczak; Qi Wang; Ivan Dikic
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.
Nature methods 2013;10(4):361-5.
2013: Roman Szczesny; Lukasz S Borowski; Krzysztof Ginalski; Monika S Hejnowicz; Anna Muszewska; Kamil Steczkiewicz; Andrzej Dziembowski
Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.
Nucleic acids research 2013;41(5):3144-61.
2012: Seweryn Mroczek; Iwo Kuciński; Krzysztof Ginalski; Joanna Krwawicz; Jan Kutner; Michal Lazniewski; Andrzej Dziembowski
C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification.
Genes & development 2012;26(17):1911-25.
2012: Kamil Steczkiewicz; Lukasz Knizewski; Anna Muszewska; Leszek Rychlewski; Krzysztof Ginalski
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
Nucleic acids research 2012;40(15):7016-45.
2011: Ewa Kurowska; Jarosław Poznański; Joanna Sasin-Kurowska; Arkadiusz Bonna; Krzysztof Ginalski; Marcin Grynberg; Lukasz Knizewski; Wojciech Bal
The C2H2 zinc finger transcription factors are likely targets for Ni(II) toxicity.
Metallomics : integrated biometal science 2011;3(11):1227-31.
2011: Kamil Steczkiewicz; Michael T Zimmermann; Drena Dobbs; Robert L Jernigan; Andrzej Kloczkowski; Andrzej Kolinski; Mateusz Kurcinski; Benjamin A Lewis; Krzysztof Ginalski
Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(23):9443-8.
2011: Michal Lazniewski; Kamil Steczkiewicz; Lukasz Knizewski; Iwona Wawer; Krzysztof Ginalski
Novel transmembrane lipases of alpha/beta hydrolase fold.
FEBS letters 2011;585(6):870-4.
2011: Dariusz Plewczynski; Michał Łaźniewski; Marcin von Grotthuss; Leszek Rychlewski; Krzysztof Ginalski
VoteDock: consensus docking method for prediction of protein-ligand interactions.
Journal of computational chemistry 2011;32(4):568-81.
2011: Dariusz Plewczynski; Michał Łaźniewski; Rafał Augustyniak; Krzysztof Ginalski
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.
Journal of computational chemistry 2011;32(4):742-55.
2011: Marcin Nowosielski; Marcin Hoffmann; Lucjan S Wyrwicz; Piotr Stepniak; Dariusz M Plewczynski; Michal Lazniewski; Krzysztof Ginalski; Leszek Rychlewski
Detailed mechanism of squalene epoxidase inhibition by terbinafine.
Journal of chemical information and modeling 2011;51(2):455-62.
2011: Tomasz Wlodarski; Andrzej Dziembowski; Lukasz Knizewski; Andrzej Kudlicki; Jan Kutner; Maga Rowicka; Leszek Rychlewski; Joanna Towpik; Krzysztof Ginalski
Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.
PloS one 2011;6(8):e23168.
2011: Pawel Szczesny; F Gisou van der Goot; Krzysztof Ginalski; Ioan Iacovache; Anna Muszewska; Marcin Grynberg
Extending the aerolysin family: from bacteria to vertebrates.
PloS one 2011;6(6):e20349.
2010: Kamil Steczkiewicz; Lukasz Knizewski; Leszek Rychlewski; Krzysztof Ginalski
TOS1 is circularly permuted 1,3-beta-glucanase.
Cell cycle (Georgetown, Tex.) 2010;9(1):201-4.
2009: Krzysztof Kuchta; Lukasz Knizewski; Lucjan S Wyrwicz; Leszek Rychlewski; Krzysztof Ginalski
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human.
Nucleic acids research 2009;37(22):7701-14.
2009: Ying Zhang; Ines Thiele; Dana Weekes; Zhanwen Li; Lukasz Jaroszewski; Krzysztof Ginalski; Ashley M Deacon; John Wooley; Scott A Lesley; Ian A Wilson; Bernhard Palsson; Andrei Osterman; Adam Godzik
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.
Science (New York, N.Y.) 2009;325(5947):1544-9.
2009: Dariusz Plewczynski; Marcin von Grotthuss; Leszek Rychlewski; Krzysztof Ginalski
Virtual high throughput screening using combined random forest and flexible docking.
Combinatorial chemistry & high throughput screening 2009;12(5):484-9.
2009: Marcin Kierczak; Krzysztof Ginalski; Michał Dramiński; Jacek Koronacki; Witold Rudnicki; Jan Komorowski
A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome.
Bioinformatics and biology insights 2009;3():109-27.
2008: Lukasz Knizewski; Krzysztof Ginalski; Andrzej Jerzmanowski
Snf2 proteins in plants: gene silencing and beyond.
Trends in plant science 2008;13(10):557-65.
2008: Jose Jimenez; Angeles Canales; Jesús Jiménez-Barbero; Krzysztof Ginalski; Leszek Rychlewski; José L García; Eduardo Díaz
Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(32):11329-34.
2008: Jan Kutner; Joanna Towpik; Krzysztof Ginalski; Magdalena Boguta
Mitochondrial release factor in yeast: interplay of functional domains.
Current genetics 2008;53(3):185-92.
2008: Lukasz Knizewski; Kamil Steczkiewicz; Krzysztof Kuchta; Lucjan Wyrwicz; Dariusz Plewczynski; Andrzej Kolinski; Leszek Rychlewski; Krzysztof Ginalski
Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases.
Cell cycle (Georgetown, Tex.) 2008;7(4):542-4.
2008: Lucjan S Wyrwicz; Krzysztof Ginalski; Leszek Rychlewski
HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein.
Cell cycle (Georgetown, Tex.) 2008;7(2):269-71.
2008: Dariusz Plewczynski; Lukasz Slabinski; Krzysztof Ginalski; Leszek Rychlewski
Prediction of signal peptides in protein sequences by neural networks.
Acta biochimica Polonica 2008;55(2):261-7.
2008: Dariusz Plewczynski; Adrian Tkacz; Lucjan S Wyrwicz; Leszek Rychlewski; Krzysztof Ginalski
AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update.
Journal of molecular modeling 2008;14(1):69-76.
2007: Lukasz Knizewski; Krzysztof Ginalski
Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding.
Cell cycle (Georgetown, Tex.) 2007;6(13):1666-70.
2007: Alexander Dikiy; Sergey V Novoselov; Dmitri E Fomenko; Aniruddha Sengupta; Bradley A Carlson; Ronald L Cerny; Krzysztof Ginalski; Nick V Grishin; Dolph L Hatfield; Vadim N Gladyshev
SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family.
Biochemistry 2007;46(23):6871-82.
2007: Dariusz Plewczynski; Marcin Hoffmann; Marcin von Grotthuss; Krzysztof Ginalski; Leszek Rychewski
In silico prediction of SARS protease inhibitors by virtual high throughput screening.
Chemical biology & drug design 2007;69(4):269-79.
2007: Dariusz Plewczynski; Marcin von Grotthuss; Stephane A H Spieser; Leszek Rychlewski; Lucjan S Wyrwicz; Krzysztof Ginalski; Uwe Koch
Target specific compound identification using a support vector machine.
Combinatorial chemistry & high throughput screening 2007;10(3):189-96.
2007: Lukasz Knizewski; Lisa N Kinch; Nick V Grishin; Leszek Rychlewski; Krzysztof Ginalski
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
BMC structural biology 2007;7():40.
2006: Kamil Steczkiewicz; Lisa N Kinch; Nick V Grishin; Leszek Rychlewski; Krzysztof Ginalski
Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily.
Cell cycle (Georgetown, Tex.) 2006;5(24):2927-30.
2006: Theodore J Lampidis; Metin Kurtoglu; Johnathan Maher; Huaping Liu; AWTAR KRISHAN; Valerie Sheft; Slawomir Szymanski; Izabela Fokt; Witold R Rudnicki; Krzysztof Ginalski; Bogdan Lesyng; Waldemar Priebe
Efficacy of 2-halogen substituted D-glucose analogs in blocking glycolysis and killing "hypoxic tumor cells".
Cancer chemotherapy and pharmacology 2006;58(6):725-34.
2006: Krzysztof Ginalski; Adam Godzik; Leszek Rychlewski
Novel SARS unique AdoMet-dependent methyltransferase.
Cell cycle (Georgetown, Tex.) 2006;5(20):2414-6.
2006: Lukasz Knizewski; Krzysztof Ginalski
DUF1613 is a novel family of eucaryotic AdoMet-dependent methyltransferases.
Cell cycle (Georgetown, Tex.) 2006;5(14):1580-2.
2006: Krzysztof Ginalski
Comparative modeling for protein structure prediction.
Current opinion in structural biology 2006;16(2):172-7.
2006: Lukasz Knizewski; Lisa N Kinch; Nick V Grishin; Leszek Rychlewski; Krzysztof Ginalski
Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease.
Journal of virology 2006;80(5):2575-7.
2006: Marcin von Grotthuss; Dariusz Plewczynski; Krzysztof Ginalski; Leszek Rychlewski; Eugene I Shakhnovich
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
BMC bioinformatics 2006;7():53.
2006: Lisa N Kinch; Krzysztof Ginalski; Nick V Grishin
Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade.
Protein science : a publication of the Protein Society 2006;15(1):84-93.
2005: Łukasz Knizewski; Krzysztof Ginalski
Bacillus subtilis YkuK protein is distantly related to RNase H.
FEMS microbiology letters 2005;251(2):341-6.
2005: Mingzhu Zheng; Krzysztof Ginalski; Leszek Rychlewski; Nick V Grishin
Protein domain of unknown function DUF1023 is an alpha/beta hydrolase.
Proteins 2005;59(1):1-6.
2005: Lisa N Kinch; Krzysztof Ginalski; Leszek Rychlewski; Nick V Grishin
Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
Nucleic acids research 2005;33(11):3598-605.
2005: Krzysztof Ginalski; Nick V Grishin; Adam Godzik; Leszek Rychlewski
Practical lessons from protein structure prediction.
Nucleic acids research 2005;33(6):1874-91.
2005: Sara Cheek; Krzysztof Ginalski; Hong Zhang; Nick V Grishin
A comprehensive update of the sequence and structure classification of kinases.
BMC structural biology 2005;5():6.
2004: Tim A Rand; Krzysztof Ginalski; Nick V Grishin; Xiaodong Wang
Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(40):14385-9.
2004: Krzysztof Ginalski; Tomasz Zemojtel
ECEPE proteins: a novel family of eukaryotic cysteine proteinases.
Trends in biochemical sciences 2004;29(10):524-6.
2004: Krzysztof Ginalski; Hong Zhang; Nick V Grishin
Raptor protein contains a caspase-like domain.
Trends in biochemical sciences 2004;29(10):522-4.
2004: Krzysztof Ginalski; Lisa N Kinch; Leszek Rychlewski; Nick V Grishin
BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases.
Trends in biochemical sciences 2004;29(8):392-5.
2004: Krzysztof Ginalski; Lisa N Kinch; Leszek Rychlewski; Nick V Grishin
DCC proteins: a novel family of thiol-disulfide oxidoreductases.
Trends in biochemical sciences 2004;29(7):339-42.
2004: Krzysztof Ginalski; Marcin von Grotthuss; Nick V Grishin; Leszek Rychlewski
Detecting distant homology with Meta-BASIC.
Nucleic acids research 2004;32(Web Server issue):W576-81.
2004: Krzysztof Ginalski; Lisa N Kinch; Leszek Rychlewski; Nick V Grishin
BOF: a novel family of bacterial OB-fold proteins.
FEBS letters 2004;567(2-3):297-301.
2004: Ceslovas Venclovas; Krzysztof Ginalski; Chulhee Kang
Sequence-structure mapping errors in the PDB: OB-fold domains.
Protein science : a publication of the Protein Society 2004;13(6):1594-602.
2004: Joanna Towpik; Agnieszka Chaciñska; Malgorzata Ciesla; Krzysztof Ginalski; Magdalena Boguta
Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes.
The Journal of biological chemistry 2004;279(14):14096-103.
2004: Krzysztof Ginalski; Leszek Rychlewski; David Baker; Nick V Grishin
Protein structure prediction for the male-specific region of the human Y chromosome.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(8):2305-10.
2003: Richard Gordon; Krzysztof Ginalski; Witold R Rudnicki; Leszek Rychlewski; Marvin C Pankaskie; Janusz Bujnicki; Peter K Chiang
Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.
European journal of biochemistry / FEBS 2003;270(17):3507-17.
2003: Krzysztof Ginalski; Jakub Paś; Lucjan S Wyrwicz; Marcin von Grotthuss; Janusz Bujnicki; Leszek Rychlewski
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure.
Nucleic acids research 2003;31(13):3804-7.
2003: Krzysztof Ginalski; Leszek Rychlewski
Detection of reliable and unexpected protein fold predictions using 3D-Jury.
Nucleic acids research 2003;31(13):3291-2.
2003: Krzysztof Ginalski; Arne Elofsson; Daniel Fischer; Leszek Rychlewski
3D-Jury: a simple approach to improve protein structure predictions.
Bioinformatics (Oxford, England) 2003;19(8):1015-8.
2003: Peter Borowski; Johanna Deinert; Sarah Schalinski; Maria Bretner; Krzysztof Ginalski; Tadeusz Kulikowski; David Shugar
Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses.
European journal of biochemistry / FEBS 2003;270(8):1645-53.
2003: Marcin von Grotthuss; Jakub Paś; Lucjan S Wyrwicz; Krzysztof Ginalski; Leszek Rychlewski
Application of 3D-Jury, GRDB, and Verify3D in fold recognition.
Proteins 2003;53 Suppl 6():418-23.
2003: Krzysztof Ginalski; Leszek Rychlewski
Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment.
Proteins 2003;53 Suppl 6():410-7.
2002: Masood Z Hadi; Krzysztof Ginalski; Lam H Nguyen; David Michael Wilson
Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.
Journal of molecular biology 2002;316(3):853-66.
2001: M Miller; Krzysztof Ginalski; Bogdan Lesyng; N Nakaigawa; L Schmidt; Berton Zbar
Structural basis of oncogenic activation caused by point mutations in the kinase domain of the MET proto-oncogene: modeling studies.
Proteins 2001;44(1):32-43.
2000: Krzysztof Ginalski; Ceslovas Venclovas; Bogdan Lesyng; Krzysztof Fidelis
Structure-based sequence alignment for the beta-trefoil subdomain of the clostridial neurotoxin family provides residue level information about the putative ganglioside binding site.
FEBS letters 2000;482(1-2):119-24.
1999: Krzysztof Ginalski; Marcin Wojciechowski; Bogdan Lesyng
Modelling of insulin receptor tyrosine kinase in its active form: a case study for validation of theoretical methods.
Acta biochimica Polonica 1999;46(3):601-7.
1999: Ceslovas Venclovas; Krzysztof Ginalski; Krzysztof Fidelis
Addressing the issue of sequence-to-structure alignments in comparative modeling of CASP3 target proteins.
Proteins 1999;Suppl 3():73-80.
1997: Krzysztof Ginalski; Bogdan Lesyng; J Sowadski; Marcin Wojciechowski
Modelling of active forms of protein kinases: p38--a case study.
Acta biochimica Polonica 1997;44(3):557-64.