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  1. Steczkiewicz K, Knizewski L, Rychlewski L, Ginalski K
    TOS1 is circularly permuted 1,3-beta-glucanase.
    Cell Cycle. 2010 Jan 1;9(1):201-4. [Library]

  2. Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ
    ELM: the status of the 2010 eukaryotic linear motif resource.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. [Library]

  3. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K
    Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human.
    Nucleic Acids Res. 2009 Dec;37(22):7701-14. [Library]

  4. Ostrowski J, Polkowski M, Paziewska A, Skrzypczak M, Goryca K, Rubel T, Kokoszynska K, Rutkowski P, Nowecki ZI, Jerzak Vel Dobosz A, Jarosz D, Ruka W, Wyrwicz LS
    Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.
    BMC Cancer 2009; 9:413. [DOI]

  5. Kokoszynska K, Krynski J, Rychlewski L, Wyrwicz LS
    Unexpected domain composition of MACC1 links MET signaling and apoptosis.
    Acta Biochim Pol. 2009; 56(2):317-23. [Library]

  6. Kubas A, Hoffmann M, Marciniec B
    Quantum chemical studies on substitution effects within silyl group in the silylative coupling of olefins.
    J Mol Model. 2010; 16:395-400. [DOI]

  7. Plewczynski D, von Grotthuss M, Rychlewski L, Ginalski K
    Virtual high throughput screening using combined random forest and flexible docking.
    Comb Chem High Throughput Screen. 2009 Jun;12 (5):484-9. [Library]

  8. Yin Y, Martin J, Abubucker S, Wang Z, Wyrwicz L, Rychlewski L, McCarter JP, Wilson RK, Mitreva M
    Molecular determinants archetypical to the phylum Nematoda.
    BMC Genomics. 2009 Mar 18;10:114. [Library]

  9. Plewczynski D, Rychlewski L
    Meta-basic estimates the size of druggable human genome.
    J Mol Model. 2009 Jun;15(6):695-699. [Library]

  10. Hoffmann M, Torchala M
    Search for inhibitors of AminoAcyl-tRNA synthases by virtual click chemistry.
    J Mol Model. 2009 Jun;15(6):665-672. [Library]

  11. Jimenez JI, Canales A, Jimenez-Barbero J, Ginalski K, Rychlewski L, Garcia JL, Diaz E
    Reply to Behrman: "N-Formylmaleamic acid: An intermediate in nicotinic acid metabolism".
    Proc Natl Acad Sci USA. 2008 Nov;105(47):E89. [DOI]

  12. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kröger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jézéquel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV
    The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
    Nature. 2008 Nov 13;456(7219):239-44. [Library]

  13. Jaroszewski L, Slabinski L, Wooley J, Deacon AM, Lesley SA, Wilson IA, Godzik A
    Genome pool strategy for structural coverage of protein families.
    Structure. 2008 Nov;16(11):1659-67. [Library]

  14. Hoffmann M, Nowosielski M
    DFT study on hydroxy acid–lactone interconversion of statins: the case of atorvastatin.
    Org Biomol Chem. 2008;6(19):3527–3531. [DOI]

  15. Kokoszynska K, Ostrowski J, Rychlewski L, Wyrwicz LS
    The fold recognition of CP2 transcription factors gives new insights into the function and evolution of tumor suppressor protein p53.
    Cell Cycle. 2008 Sep 15;7(18):2907-15. [DOI]

  16. Jimenez JI, Canales A, Jimenez-Barbero J, Ginalski K, Rychlewski L, Garcia JL, Diaz E
    Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440.
    Proc Natl Acad Sci USA. 2008 Aug 12;105(32):11329-34. [Library]

  17. Plewczynski D, Slabinski L, Ginalski K, Rychlewski L
    Prediction of signal peptides in protein sequences by neural networks.
    Acta Biochim Pol. 2008;55(2):261-7. [Library]

  18. Wyrwicz LS, Rychlewski L
    Cytomegalovirus immediate early gene UL37 encodes a novel MHC-like protein.
    Acta Biochim Pol. 2008;55(1):67-73. [Library]

  19. Knizewski L, Steczkiewicz K, Kuchta K, Wyrwicz L, Plewczynski D, Kolinski A, Rychlewski L, Ginalski K
    Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases.
    Cell Cycle. 2008 Feb;7(4):542-4. [Library]

  20. Wyrwicz LS, Ginalski K, Rychlewski L
    HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein.
    Cell Cycle. 2008 Jan;7(2):269-71. [Library]

  21. Plewczynski D, Tkacz A, Wyrwicz LS, Rychlewski L, Ginalski K
    AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update.
    J Mol Model. 2008 Jan;14(1):69-76. [Library]

  22. Kokoszynska K, Rychlewski L, Wyrwicz LS
    The mitotic entry regulator NIPA is a prototypic BIR domain protein.
    Cell Cycle. 2008 Jul;7(13):2073-5. [Library]

  23. von Grotthuss M, Plewczynski D, Vriend G, Rychlewski L
    3D-Fun: predicting enzyme function from structure.
    Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W303-7. [Library]

  24. Wyrwicz LS, Koczyk G, Rychlewski L
    Homologues of HSV-1 nuclear egress factor UL34 are potential phosphoinositide-binding proteins.
    Acta Biochim Pol. 2008;55(1):207-13. [Library]

  25. Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A
    XtalPred: a web server for prediction of protein crystallizability.
    Bioinformatics. 2007 Dec 15;23(24):3403-5. [Library]

  26. Jura M, Rychlewski L, Barciszewski J
    Comprehensive insight into human aminoacyl-tRNA synthetases as autoantigens in idiopathic inflammatory myopathies.
    Crit Rev Immunol. 2007;27(6):559-72. [Library]

  27. Slabinski L, Jaroszewski L, Rodrigues APC, Rychlewski L, Wilson IA, Lesley SA, Godzik A
    The challenge of protein structure determination - lessons from structural genomics.
    Protein Sci. 2007 Nov;16(11):2472-82. [Library]

  28. Wyrwicz LS, Rychlewski L
    Fold recognition insights into function of herpes ICP4 protein.
    Acta Biochim Pol. 2007;54(3):551-9. [Library]

  29. Plewczynski D, Slabinski L, Tkacz A, Kajan L, Holm L, Ginalski K, Rychlewski L
    The RPSP: web server for prediction of signal peptides.
    Polymer. 2007;48(19):5493-5496. [DOI]

  30. Fiszer D, Rozwadowska N, Rychlewski L, Kosicki W, Kurpisz M
    Identification of IL-18RAP mRNA truncated splice variants in human testis and the other human tissues.
    Cytokine. 2007 Sep;39(3):178-83. [DOI]

  31. Torchala M, Hoffmann M
    IA, database of known ligands of aminoacyl-tRNA synthetases.
    J Comput Aided Mol Des. 2007 Sep 20;21(9):523-5. [Library]

  32. Kajan L, Rychlewski L
    Evaluation of 3D-Jury on CASP7 models.
    BMC Bioinformatics. 2007 Aug 21;8:304. [Library]

  33. Plewczynski D, Hoffmann M, von Grotthuss M, Knizewski L, Rychewski L, Eitner K, Ginalski K
    Modelling of potentially promising SARS protease inhibitors.
    J Phys Cond Matter. 2007;19(28):285207. [DOI]

  34. Wyrwicz LS, Koczyk G, Rychlewski L, Plewczynski D
    ProteinSplit: Splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics.
    J Phys Cond Matter. 2007;19(28):285222. [DOI]

  35. Wyrwicz LS, Rychlewski L
    Identification of Herpes TATT-binding protein.
    Antiviral Res. 2007 Aug;75(2):167-72. [Library]

  36. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K
    Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
    BMC Struct Biol. 2007 Jun 20;7(1):40. [Library]

  37. Wyrwicz LS, Rychlewski L
    Herpes glycoprotein gL is distantly related to chemokine receptor ligands.
    Antiviral Res. 2007 Jul;75(1):83-6. [Library]

  38. Perla-Kajan J, Marczak L, Kajan L, Skowronek P, Twardowski T, Jakubowski H
    Modification by homocysteine thiolactone affects redox status of cytochrome C.
    Biochemistry. 2007 May 29;46(21):6225-31. [Library]

  39. Masojc B, Medrek K, Debniak T, Lubinski J, Wyrwicz LS, Koczyk G, Hoffmann M, Rychlewski L
    ARLTS1 Trp149Stop Mutation and the Risk of Ovarian Cancer.
    Cancer Res. 2007 May 1;67(9):4533. [Library]

  40. Plewczynski D, Hoffmann M, von Grotthuss M, Ginalski K, Rychewski L
    In Silico Prediction of SARS Protease Inhibitors by Virtual High Throughput Screening.
    Chem Biol Drug Des. 2007 Apr;69(4):269-79. [Library]

  41. Hoffmann M, Marciniec B
    Quantum chemical study of the mechanism of ethylene elimination in silylative coupling of olefins.
    J Mol Model. 2007 Apr;13(4):477-83. [Library]

  42. Wyrwicz LS, Gaj P, Hoffmann M, Rychlewski L, Ostrowski J
    A common cis-element in promoters of protein synthesis and cell cycle genes.
    Acta Biochim Pol. 2007 Mar 9;54(1):89-98. [Library]

  43. Plewczynski D, von Grotthuss M, Spieser SA, Rychlewski L, Wyrwicz LS, Ginalski K, Koch U
    Target specific compound identification using a support vector machine.
    Comb Chem High Throughput Screen. 2007 Mar;10(3):189-96. [Library]

  44. Koczyk G, Wyrwicz LS, Rychlewski L
    LigProf: a simple tool for in silico prediction of ligand-binding sites.
    J Mol Model. 2007 Mar;13(3):445-55. [Library]

  45. Eitner K, Gaweda T, Hoffmann M, Jura M, Rychlewski L, Barciszewski J
    eHiTS-to-VMD Interface Application. The Search for Tyrosine-tRNA Ligase Inhibitors.
    J Chem Inf Model. 2007 Mar 26;47(2):695-702. [Library]

  46. Slabinski L, Godzik A, Rychlewski L
    TOM - Task and Object Management for Grid Clusters.
    Proceedings of the 2007 International Conference on Grid Computing and Applications (GCA'07). ISBN: 1-60132-032-9. [DOI]

  47. Steczkiewicz K, Kinch L, Grishin NV, Rychlewski L, Ginalski K
    Eukaryotic Domain of Unknown Function DUF738 Belongs to Gcn5-related N-acetyltransferase Superfamily.
    Cell Cycle. 2006 Dec 15;5(24):2927-30. [Library]

  48. Grabarkiewicz T, Grobelny P, Hoffmann M, Mielcarek J
    DFT study on hydroxy acid-lactone interconversion of statins: The case of fluvastatin.
    Org Biomol Chem. 2006 Dec 7;4(23):4299-306. [Library]

  49. Wyszko E, Nowak M, Pospieszny H, Szymanski M, Pas J, Barciszewska MZ, Barciszewski J
    Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum.
    FEBS J. 2006 Nov;273(22):5022-31. [Library]

  50. Zemojtel T, Frohlich A, Palmieri MC, Kolanczyk M, Mikula I, Wyrwicz LS, Wanker EE, Mundlos S, Vingron M, Martasek P, Durner J
    Plant nitric oxide synthase: a never-ending story?
    Trends Plant Sci. 2006 Nov;11(11):524-5. [Library]

  51. Ginalski K, Godzik A, Rychlewski L
    Novel SARS Unique AdoMet-Dependent Methyltransferase.
    Cell Cycle. 2006 Oct 16;5 (20):2414-16. [Library]

  52. Plewczynski D, Tkacz A, Wyrwicz LS, Godzik A, Kloczkowski A, Rychlewski L
    Support-vector-machine classification of linear functional motifs in proteins.
    J Mol Model. 2006 Mar;12(4):453-61. [Library]

  53. Pas J, Wyszko E, Rolle K, Rychlewski L, Nowak S, Zukiel R, Barciszewski J
    Analysis of structure and function of tenascin-C.
    Int J Biochem Cell Biol. 2006;38(9):1594-602. [Library]

  54. Hoffmann M, Eitner K, von Grotthuss M, Rychlewski L, Banachowicz E, Grabarkiewicz T, Szkoda T, Kolinski A
    Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.
    J Comput Aided Mol Des. 2006 May;20(5):305-19. [Library]

  55. Plewczynski D, Spieser SA, Koch U
    Assessing different classification methods for virtual screening.
    J Chem Inf Model. 2006 May-Jun;46(3):1098-106. [Library]

  56. Sikorska E, Khmelinskii I, Kubicki M, Prukala W, Hoffmann M, Machado IF, Ferreira LF, Karolczak J, Worrall DR, Krawczyk A, Insinska-Rak M, Sikorski M
    In search of excited-state proton transfer in the lumichrome dimer in the solid state: theoretical and experimental approach.
    J Phys Chem A. 2006 Apr 13;110(14):4638-48. [Library]

  57. Wagner W, Walczak-Drzewiecka A, Slusarczyk A, Biecek P, Rychlewski L, Dastych J
    Fluorescent Cell Chip a new in vitro approach for immunotoxicity screening.
    Toxicol Lett. 2006 Mar 15;162(1):55-70. [Library]

  58. von Grotthuss M, Rychlewski L
    Influenza mutation from equine to canine.
    Science. 2006 Mar 3;311(5765):1241-2. [Library]

  59. Knizewski L, Kinch L, Grishin NV, Rychlewski L, Ginalski K
    Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease.
    J Virol. 2006 Mar;80(5):2575-7. [Library]

  60. von Grotthuss M, Plewczynski D, Ginalski K, Rychlewski L, Shakhnovich EI
    PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
    BMC Bioinformatics. 2006 Feb 6;7:53. [Library]

  61. Grabarkiewicz T, Hoffmann M
    Syn- and anti-conformations of 5′-deoxy- and 5′-O-methyl-uridine 2′,3′-cyclic monophosphate.
    J Mol Model. 2006;12(2):205-12. [DOI]

  62. Sikorska E, Khmelinskii I, Hoffmann M, Machado IF, Ferreira LF, Dobek K, Karolczak J, Krawczyk A, Insińska-Rak M, Sikorski M
    Ground- and excited-state double proton transfer in lumichrome/acetic acid system: theoretical and experimental approach.
    J Phys Chem A. 2005 Dec 29;109(51):11707-14. [Library]

  63. Ginalski K, Grishin NV, Godzik A, Rychlewski L
    Practical lessons from protein structure prediction.
    Nucleic Acids Res. 2005 Apr 1;33(6):1874-91. [Library]

  64. Plewczynski D, Jaroszewski L, Godzik A, Kloczkowski A, Rychlewski L
    Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.
    J Mol Model. 2005 Nov;11(6):431-8. [Library]

  65. Kinch LN, Ginalski K, Rychlewski L, Grishin NV
    Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
    Nucleic Acids Res. 2005 Jun 22;33(11):3598-605. [Library]

  66. Paziewska A, Wyrwicz LS, Ostrowski J
    The binding activity of yeast RNAs to yeast hek2p and mammalian hnRNP K proteins, determined using the three-hybrid system.
    Cell Mol Biol Lett. 2005;10(2):227-35. [DOI]

  67. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A
    FFAS03: a server for profile-profile sequence alignments.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8. [Library]

  68. Hoffmann M
    Quantum chemical study on chiral recognition modes between esters of α-hydroxycarboxylic acids and amino acids.
    Polish J Chem. 2005;79(7):1179-85. [DOI]

  69. Hoffmann M, Chrzanowska M, Hermann T, Rychlewski J
    Modeling of purine derivatives transport across cell membranes based on their partition coefficient determination and quantum chemical calculations.
    J Med Chem. 2005 Jun 30;48(13):4482-6. [Library]

  70. Hoffmann M, Plutecka A, Rychlewska U, Kucybala Z, Paczkowski J, Pyszka I
    New Type of Bonding Formed from an Overlap between PI Aromatic and PI C=O Molecular Orbitals Stabilizes the Coexistence in One Molecule of the Ionic and Neutral meso-Ionic Forms of Imidazopyridine.
    J Phys Chem A. 2005 May 26;109(20):4568-74. [Library]

  71. Plewczynski D, Tkacz A, Wyrwicz LS, Rychlewski L
    AutoMotif Server: prediction of single residue post-translational modifications in proteins.
    Bioinformatics. 2005 May 15;21(10):2525-7. [Library]

  72. Plewczynski D, Tkacz A, Godzik A, Rychlewski L
    A support vector machine approach to the identification of phosphorylation sites.
    Cell Mol Biol Lett. 2005;10(1):73-89. [Library]

  73. Zheng M, Ginalski K, Rychlewski L, Grishin NV
    Protein domain of unknown function DUF1023 is an α/β hydrolase.
    Proteins. 2005 Feb 1;59(1):1-6. [Library]

  74. Hoffmann M, Rychlewska U, Warzajtis B
    The role of multiple parallel and antiparallel local dipoles for molecular structure and intermolecular interactions of oxalamides.
    Cryst Eng Comm. 2005;7(41):260-5. [DOI]

  75. Barciszewska MZ, Szymanski M, Wyszko E, Pas J, Rychlewski L, Barciszewski J
    Lead toxicity through the leadzyme.
    Mutat Res. 2005 Mar;589(2):103-10. [Library]

  76. Rychlewski L, Fischer D
    LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction.
    Protein Sci. 2005 Jan;14(1):240-5. [Library]

  77. Ostrowski J, Klimek-Tomczak K, Wyrwicz LS, Mikula M, Schullery DS, Bomsztyk K
    Heterogeneous nuclear ribonucleoprotein K enhances insulin-induced expression of mitochondrial UCP2 protein.
    J Biol Chem. 2004 Dec 24;279(52):54599-609. [Library]

  78. von Grotthuss M, Koczyk G, Pas J, Wyrwicz LS, Rychlewski L
    Ligand.Info small-molecule Meta-Database.
    Comb Chem High Throughput Screen. 2004 Dec;7(8):757-61. [Library]

  79. Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J
    Cooperative binding of the hnRNP K three KH domains to mRNA targets.
    FEBS Lett. 2004 Nov 5;577(1-2):134-40. [Library]

  80. Pas J, von Grotthuss M, Wyrwicz LS, Rychlewski L, Barciszewski J
    Structure prediction, evolution and ligand interaction of CHASE domain.
    FEBS Lett. 2004 Oct 22;576(3):287-90. [Library]

  81. Fischer D, Pas J, Rychlewski L
    The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.
    Bioinformatics. 2004 Oct 12;20(15):2482-4. [Library]

  82. Ginalski K, Zemojtel T
    ECEPE proteins: a novel family of eukaryotic cysteine proteinases.
    Trends Biochem Sci. 2004 Oct;29(10):524-6. [Library]

  83. Ginalski K, Zhang H, Grishin NV
    Raptor protein contains a caspase-like domain.
    Trends Biochem Sci. 2004 Oct;29(10):522-4. [Library]

  84. Klimek-Tomczak K, Wyrwicz LS, Jain S, Bomsztyk K, Ostrowski J
    Characterization of hnRNP K protein-RNA interactions.
    J Mol Biol. 2004 Sep 24;342(4):1131-41. [Library]

  85. Ginalski K, Kinch L, Rychlewski L, Grishin NV
    BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases.
    Trends Biochem Sci. 2004 Aug;29(8):392-5. [Library]

  86. Plewczynski D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A
    Integrated web service for improving alignment quality based on segments comparison.
    BMC Bioinformatics. 2004 Jul 22;5(1):98. [Library]

  87. Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L
    Detecting distant homology with Meta-BASIC.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W576-81. [Library]

  88. Ginalski K, Kinch L, Rychlewski L, Grishin NV
    DCC proteins: a novel family of thiol-disulfide oxidoreductases.
    Trends Biochem Sci. 2004 Jul;29(7):339-42. [Library]

  89. von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L
    Predicting protein structures accurately.
    Science. 2004 Jun 11;304(5677):1597-9. [Library]

  90. Ginalski K, Kinch L, Rychlewski L, Grishin NV
    BOF: a novel family of bacterial OB-fold proteins.
    FEBS Lett. 2004 Jun 4;567(2-3):297-301. [Library]

  91. Venclovas C, Ginalski K, Kang C
    Sequence-structure mapping errors in the PDB: OB-fold domains.
    Protein Sci. 2004 Jun;13(6):1594-602. [Library]

  92. Plewczynski D, Pas J, von Grotthuss M, Rychlewski L
    Comparison of proteins based on segments structural similarity.
    Acta Biochim Pol. 2004;51(1):161-72. [Library]

  93. Narozna D, Pas J, Schneider J, Madrzak CJ
    Two sequences encoding chalcone synthase in yellow lupin (Lupinus luteus l.) may have evolved by gene duplication.
    Cell Mol Biol Lett. 2004;9(1):95-105. [Library]

  94. Towpik J, Chacinska A, Ciesla M, Ginalski K, Boguta M
    Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes.
    J Biol Chem. 2004 Apr 2;279(14):14096-103. [Library]

  95. Rescalli E, Saini S, Bartocci C, Rychlewski L, De Lorenzo V, Bertoni G
    Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures.
    J Biol Chem. 2004 Feb 27;279(9):7777-84. [Library]

  96. Ginalski K, Rychlewski L, Baker D, Grishin NV
    Protein structure prediction for the male-specific region of the human Y chromosome.
    Proc Natl Acad Sci USA. 2004 Feb 24;101(8):2305-10. [Library]

  97. Rychlewski L, Kschischo M, Dong L, Schutkowski M, Reimer U
    Target specificity analysis of the Abl kinase using peptide microarray data.
    J Mol Biol. 2004 Feb 13;336(2):307-11. [Library]

  98. Rand TA, Ginalski K, Grishin NV, Wang X
    Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity.
    Proc Natl Acad Sci USA. 2004 Oct 5;101 (40):14385-9. [Library]

  99. Wyrwicz LS, von Grotthuss M, Pas J, Rychlewski L
    How unique is the rice transcriptome?
    Science. 2004 Jan 9;303(5655):168. [Library]

  100. Ginalski K, Rychlewski L
    Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment.
    PROTEINS: Structure, Function, and Genetics. 2003;53 Suppl 6:410-7. [Library]

  101. Fischer D, Rychlewski L, Dunbrack RL Jr, Ortiz AR, Elofsson A
    CAFASP3: the third critical assessment of fully automated structure prediction methods.
    PROTEINS: Structure, Function, and Genetics. 2003;53 Suppl 6:503-16. [Library]

  102. Rychlewski L, Fischer D, Elofsson A
    LiveBench-6: large-scale automated evaluation of protein structure prediction servers.
    PROTEINS: Structure, Function, and Genetics. 2003;53 Suppl 6:542-7. [Library]

  103. von Grotthuss M, Pas J, Wyrwicz L, Ginalski K, Rychlewski L
    Application of 3D-Jury, GRDB, and Verify3D in fold recognition.
    PROTEINS: Structure, Function, and Genetics. 2003;53 Suppl 6:418-23. [Library]

  104. Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz LS, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ
    ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
    Nucleic Acids Res. 2003 Jul 1;31(13):3625-30. [Library]

  105. Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, Rychlewski L
    ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure.
    Nucleic Acids Res. 2003 Jul 1;31(13):3804-7. [Library]

  106. Ginalski K, Rychlewski L
    Detection of reliable and unexpected protein fold predictions using 3D-Jury.
    Nucleic Acids Res. 2003 Jul 1;31(13):3291-2. [Library]

  107. von Grotthuss M, Wyrwicz LS, Rychlewski L
    mRNA cap-1 methyltransferase in the SARS genome.
    Cell. 2003 Jun 13;113(6):701-2. [Library]

  108. Ginalski K, Elofsson A, Fischer D, Rychlewski L
    3D-Jury: a simple approach to improve protein structure predictions.
    Bioinformatics. 2003 May 22;19(8):1015-8. [Library]

  109. von Grotthuss M, Pas J, Rychlewski L
    Ligand-Info, searching for similar small compounds using index profiles.
    Bioinformatics. 2003 May 22;19(8):1041-2. [Library]

  110. Borowski P, Deinert J, Schalinski S, Bretner M, Ginalski K, Kulikowski T, Shugar D
    Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses.
    Eur J Biochem. 2003 Apr;270(8):1645-53. [Library]

  111. Fischer D, Rychlewski L
    The 2002 Olympic Games of protein structure prediction.
    Protein Eng. 2003 Mar;16(3):157-60. [Library]

  112. Feder M, Pas J, Wyrwicz LS, Bujnicki JM
    Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases.
    Gene. 2003 Jan 2;302(1-2):129-38. [Library]

  113. Vanrobaeys F, Devreese B, Lecocq E, Rychlewski L, De Smet L, Van Beeumen J
    Proteomics of the dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1, using a matrix-assisted laser desorption/ionization-tandem-time of flight mass spectrometer.
    Proteomics. 2003 Nov;3(11):2249-57. [Library]

  114. Gordon RK, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie MC, Bujnicki JM, Chiang PK
    Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.
    Eur J Biochem. 2003 Sep;270(17):3507-17. [Library]

  115. Bujnicki J, Rychlewski L, Fischer D
    Fold-recognition detects an error in the Protein Data Bank.
    Bioinformatics. 2002 Oct;18(10):1391-5. [Library]

  116. Bujnicki JM, Leach RA, Debski J, Rychlewski L
    Bioinformatic analyses of the tRNA: (guanine 26,N2,N2)-dimethyltransferase (Trm1) family.
    J Mol Microbiol Biotechnol. 2002 Jul;4(4):405-15. [Library]

  117. Bujnicki JM, Rychlewski L
    Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases.
    DNA Repair. 2002 May 30;1(5):391-5. [Library]

  118. Bujnicki JM, Rychlewski L
    In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses.
    Protein Eng. 2002 Feb;15(2):101-8. [Library]

  119. Bujnicki JM, Rychlewski L
    RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
    BMC Bioinformatics. 2002 Apr 03;3(1):10. [Library]

  120. Ostrowski J, Wyrwicz L, Rychlewski L, Bomsztyk K
    Heterogeneous nuclear ribonucleoprotein K protein associates with multiple mitochondrial transcripts within the organelle.
    J Biol Chem. 2002 Feb 22;277(8):6303-10. [Library]

  121. Plewczynski D, Pas J, von Grotthuss M, Rychlewski L
    3D-Hit: fast structural comparison of proteins.
    Appl Bioinformatics. 2002;1(4):223-5. [Library]

  122. Hadi MZ, Ginalski K, Nguyen LH, Wilson DM 3rd
    Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.
    J Mol Biol. 2002 Feb 22;316(3):853-66. [Library]

  123. Bujnicki JM, Blumenthal RM, Rychlewski L
    Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus.
    J Mol Microbiol Biotechnol. 2002 Jan;4(1):93-9. [Library]

  124. Rychlewski L
    ToolShop: prerelease inspections for protein structure prediction servers.
    Bioinformatics. 2001 Dec;17(12):1240-1. [Library]

  125. Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L
    Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
    Protein Eng. 2001 Oct;14(10):717-21. [Library]

  126. Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL Jr
    CAFASP2: the second critical assessment of fully automated structure prediction methods.
    PROTEINS: Structure, Function, and Genetics. 2001;Suppl 5:171-83. [Library]

  127. Bujnicki JM
    Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons.
    Acta Biochim Pol. 2001;48(4):935-67. [DOI]

  128. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L
    LiveBench-2: large-scale automated evaluation of protein structure prediction servers.
    PROTEINS: Structure, Function, and Genetics. 2001;Suppl 5:184-91. [Library]

  129. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L
    Structure prediction meta server.
    Bioinformatics. 2001 Aug;17(8):750-1. [Library]

  130. Bujnicki JM, Feder M, Radlinska M, Rychlewski L
    mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
    BMC Bioinformatics. 2001;2(1):2. [Library]

  131. Bujnicki JM, Rychlewski L
    Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein.
    Genome Biol. 2001;2(9):RESEARCH0038. [Library]

 
 
 


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