Publikacijos

2017

  • Dapkūnas J, Timinskas A, Olechnovič K, Margelevičius M, Dičiūnas R, Venclovas Č. (2017) The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures. Bioinformatics [PubMed]

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  • Tamulaitis G, Venclovas Č, Šiksnys V. (2017) Type III CRISPR-Cas immunity: major differences brushed aside. Trends Microbiol, 25:49-61 [PubMed]

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2016

  • Venclovas Č. (2016) Structure of Csm2 elucidates the relationship between small subunits of CRISPR-Cas effector complexes. FEBS Lett, 590:1521-9 [PubMed]

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  • Kazlauskas D, Krupovic M, Venclovas Č. (2016) The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes. Nucleic Acids Res, 44:4551-64[PubMed]

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  • Kazlauskiene M, Tamulaitis G, Kostiuk G, Venclovas Č, Siksnys V. (2016) Spatiotemporal control of Type III-A CRISPR-Cas immunity: coupling DNA degradation with the target RNA recognition. Mol Cell, 62:295-306 [PubMed]

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2015

  • Achar YJ, Balogh D, Neculai D, Juhasz S, Morocz M, Gali H, Dhe-Paganon S, Venclovas Č, Haracska L. (2015) Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling. Nucleic Acids Res, 43:10277-91 [PubMed]

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  • Baranauskė S, Mickutė M, Plotnikova A, Finke A, Venclovas Č, Klimašauskas S, Vilkaitis G. (2015) Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Res, 43:2802-2812 [PubMed]

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  • Zilnyte M, Venclovas Č, Zvirbliene A, Pleckaityte M. (2015) The cytolytic activity of vaginolysin strictly depends on cholesterol and is potentiated by human CD59. Toxins, 7:110-128. [PubMed]

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2014

  • Tamulaitis G, Kazlauskiene M, Manakova E, Venclovas Č, Nwokeoji AO, Dickman MJ, Horvath P, Siksnys V. (2014) Programmable RNA Shredding by the Type III-A CRISPR-Cas System ofStreptococcus thermophilus. Mol Cell, 56:506-517. [PubMed]

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  • Kazlauskas D, Venclovas Č. (2014) Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase. Bioinformatics, 30(15):2093-2097. [PubMed]

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  • Olechnovič K, Venclovas Č. (2014) The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes. Nucleic Acids Res,42(Web Server issue):W259-W263 [PubMed] NAR Breakthrough Article

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  • Olechnovič K, Venclovas Č. (2014) The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures. Nucleic Acids Res, 42:5407-5415 [PubMed]

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  • Fang J, Nevin P, Kairys V, Venclovas Č, Engen JR, Beuning PJ. (2014) Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics. Structure, 22:572-581 [PubMed]

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  • Olechnovič K, Venclovas Č. (2014) Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls. J Comput Chem, 35:672-81 [PubMed]

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  • Timinskas K, Balvočiūtė M, Timinskas A, Venclovas Č. (2014) Comprehensive analysis of DNA polymerase III alpha subunits and their homologs in bacterial genomes. Nucleic Acids Res, 42:1393-1413 [PubMed]

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2013

  • Gopinath K, Venclovas Č, Ioerger TR, Sacchettini JC, McKinney JD, Mizrahi V, Warner DF. (2013) A vitamin B12 transporter in Mycobacterium tuberculosis. Open Biol, 3:120175. [PubMed]

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  • Olechnovič K, Kulberkytė E, Venclovas Č. (2013) CAD-score: A new contact area difference-based function for evaluation of protein structural models. Proteins, 81:149–162. [PubMed]

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2012

  • Kazlauskas D, Venclovas Č. (2012) Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses. Bioinformatics, 28: 3186-3190. [PubMed]

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  • Nagirnaja L, Venclovas Č, Rull K, Jonas KC, Peltoketo H, Christiansen OB, Kairys V, Kivi G, Steffensen R, Huhtaniemi IT, Laan M. (2012) Structural and functional analysis of rare missense mutations in human chorionic gonadotropin beta-subunit. Mol Hum Reprod, 18:379-390. [PubMedFeatured as a cover story

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  • Venclovas Č. (2012) Methods for sequence-structure alignment. Methods Mol Biol, 857:55-82. [PubMed]

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2011

  • Timinskas K, Venclovas Č. (2011) The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III tau subunit.FEBS J, 278:3109-3118. [PubMed]

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  • Kazlauskas D, Venclovas Č. (2011) Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size. Nucleic Acids Res, 39:8291-305. [PubMed]

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  • Olechnovič K, Margelevičius M, Venclovas Č. (2011) Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure. Bioinformatics, 27:723-724.[PubMed]

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  • Laganeckas M, Margelevičius M, Venclovas Č. (2011) Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.Nucleic Acids Res, 39:1187-1196. [PubMed]

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  • Barsky D, Laurence TA, Venclovas Č. (2011) How proteins slide on DNA. In Biophysics of DNA-protein interactions: From single molecules to biological systems, M.C. Williams and Maher, L.J. III, eds., Springer Science + Business Media, LLC, p.39-68. [Publisher link]

2010

  • Warner DF, Ndwandwe DE, Abrahams GL, Kana BD, Machowski EE, Venclovas Č, Mizrahi V. (2010) Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci USA, 107:13093-13098. [PubMed]

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  • Margelevičius M, Laganeckas M, and Venclovas Č. (2010) COMA server for protein distant homology search. Bioinformatics, 26:1905-1906. [PubMed]

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  • Margelevičius M and Venclovas Č. (2010) Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. BMC Bioinformatics, 11:89.[PubMed]

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  • Zubrienė A, Gutkowska M, Matulienė J, Chaleckis R, Michailovienė V, Voroncova A, Venclovas Č, Zylicz A, Zylicz M, Matulis D. (2010) Thermodynamics of radicicol binding to human Hsp90 alpha and beta isoforms. Biophys Chem, 152:153-163. [PubMed]

 

2009

  • Venclovas Č and Margelevičius M. (2009) The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins. Proteins, 77 Suppl 9:81-88. [ PubMed]

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2008

  • McCauley MJ, Shokri L, Sefcikova J, Venclovas Č, Beuning PJ, Williams M. (2008) Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit. ACS Chem Biol, 3:577-587. [ PubMed]

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  • Repšys V, Margelevičius M, and Venclovas Č. (2008) Re-searcher: a system for recurrent detection of homologous protein sequences. BMC Bioinformatics, 9:296. [PubMed]

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2007

  • Jurėnaitė-Urbanavičienė S, Šerkšnaitė J, Kriukienė E, Giedrienė J, Venclovas Č, Lubys A. (2007) Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. Proc Natl Acad Sci USA, 104:10358-10363. [PubMed]

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  • Sukackaite R, Lagunavicius A, Stankevicius K, Urbanke C, Venclovas Č, Siksnys V. (2007) Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family. Nucleic Acids Res., 35:2377-2389. [PubMed]

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2006

  • Shi G, Chang DY, Cheng CC, Guan X, Venclovas Č, Lu A-L. (2006) Physical and functional interactions between MutY homolog (MYH) and checkpoint proteins Rad9-Rad1-Hus1. Biochem J., 400:53-62. [PubMed]

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2005

  • Barsky D, Venclovas Č. (2005) DNA sliding clamps: just the right twist to load onto DNA. Curr Biol. 15:R989-R992. [PubMed]

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  • Venclovas Č, Margelevičius M. (2005) Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment and structure assessment. Proteins, 61 Suppl 7:99-105. [PubMed]

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  • Kryshtafovych A, Venclovas Č, Fidelis K, Moult J. (2005) Progress over the first decade of CASP experiments. Proteins, 61 Suppl 7:225-36. [PubMed]

 

  • Margelevičius M, Venclovas Č. (2005) PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. BMC Bioinformatics, 6:185. [PubMed]

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2004

  • Daujotytė D, Serva S, Vilkaitis G, Merkienė E, Venclovas Č, Klimašauskas S. (2004) HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine. Structure, 12:1047-55. [PubMed]

 

  • Venclovas Č, Ginalski K, Kang C. (2004) Sequence-structure mapping errors in the PDB: OB-fold domains. Protein Sci, 13:1594-1602. [PubMed]

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2003

  • Venclovas Č. (2003) Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance. Proteins, 53, Suppl 6: 380-388. [PubMed]

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  • Venclovas Č, Zemla A, Fidelis K, Moult J. (2003) Assessment of progress over the CASP experiments. Proteins, 53, Suppl 6:585-595. [PubMed]

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  • Winthrop MD, DeNardo SJ, Albrecht H, Mirick GR, Kroger LA, Lamborn KR, Venclovas Č, Colvin ME, Burke PA, DeNardo GL. (2003) Selection and characterization of anti-MUC-1 scFvs intended for targeted therapy. Clinical Cancer Research, 9 (10 Pt 2):3845S-3853S. [PubMed]

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2002

  • Venclovas Č, Colvin ME, Thelen MP. (2002) Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process. Protein Sci., 11: 2403-2416. [PubMed]

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  • Bitinaitė J, Mitkaitė G, Daukšaitė V, Jakubauskas A, Timinskas A, Vaišvila R, Lubys A, Janulaitis A. (2002) Evolutionary relationship of Alw26I, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences. Mol Genet Genomics, 267:664-672. [PubMed]

 

  • Vilkaitis G, Lubys A, Merkienė E, Timinskas A, Janulaitis A, Klimašauskas S. (2002) Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation. Nucleic Acids Res. 30:1547-1557 [PubMed]

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2001

  • Venclovas Č, Zemla A, Fidelis K, Moult J. (2001) Comparison of performance in successive CASP experiments. Proteins, Suppl. 5:163-170 [PubMed]

 

  • Venclovas Č. (2001) Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment. Proteins, Suppl. 5:47-54. [PubMed]

 

  • Česnavičienė E, Petrušytė M, Kazlauskienė R, Manelienė Z, Timinskas A, Lubys A, Janulaitis A. (2001) Characterization of AloI, a restriction-modification system of a new type. J Mol Biol. 314:205-216. [PubMed]

 

  • Vitkutė J, Stankevičius K, Tamulaitienė G, Manelienė Z, Timinskas A, Berg DE, Janulaitis A. (2001) Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695. J Bacteriol. 183:443-450.[PubMed]

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2000

  • Ginalski K, Venclovas Č, Lesyng B, Fidelis K. (2000) Structure-based sequence alignment for the beta-trefoil sub-domain of the clostridial neurotoxin family provides residue level information about the putative ganglioside binding site. FEBS Lett., 482:119-124. [PubMed]

 

  • Venclovas Č, Thelen M. (2000) Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes. Nucleic Acids Res., 28:2481-2493.[PubMed]

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1999

  • Venclovas Č, Ginalski K, Fidelis K. (1999) Addressing the issue of sequence-to-structure alignments in comparative modeling of CASP3 target proteins. Proteins, Suppl. 3:73-80. [PubMed]

 

  • Venclovas Č, Zemla A, Fidelis K, Moult J. (1999) Some measures of comparative performance in the three CASPs. Proteins, Suppl. 3: 231-237. [PubMed]

 

  • Zemla A, Venclovas Č, Moult J, Fidelis K. (1999) Processing and Analysis of CASP3 Protein Structure Predictions. Proteins, Suppl. 3:22-29. [PubMed]

 

  • Thelen M, Venclovas Č, Fidelis K. (1999) A sliding clamp model for the Rad1 family of cell cycle checkpoint proteins. Cell, 96:769-770. [PubMed]

 

  • Zemla A, Venclovas Č, Fidelis K, Rost B. (1999) A modified definition of Sov, a segment based measure for protein secondary structure prediction assessment. Proteins, 34:220-223. [PubMed]