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Items: 1 to 50 of 67

1.

DnaQ exonuclease-like domain of Cas2 promotes spacer integration in a type I-E CRISPR-Cas system.

Drabavicius G, Sinkunas T, Silanskas A, Gasiunas G, Venclovas Č, Siksnys V.

EMBO Rep. 2018 Jun 11. pii: e45543. doi: 10.15252/embr.201745543. [Epub ahead of print]

PMID:
29891635
2.

The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.

Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M.

Nucleic Acids Res. 2018 Mar 16;46(5):2560-2572. doi: 10.1093/nar/gky107.

3.

Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.

Kazlauskas D, Sezonov G, Charpin N, Venclovas Č, Forterre P, Krupovic M.

J Mol Biol. 2018 Mar 2;430(5):737-750. doi: 10.1016/j.jmb.2017.11.014. Epub 2017 Dec 11.

4.

Modeling of protein complexes in CAPRI Round 37 using template-based approach combined with model selection.

Dapkūnas J, Olechnovič K, Venclovas Č.

Proteins. 2018 Mar;86 Suppl 1:292-301. doi: 10.1002/prot.25378. Epub 2017 Sep 23.

PMID:
28905467
5.

A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems.

Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V.

Science. 2017 Aug 11;357(6351):605-609. doi: 10.1126/science.aao0100. Epub 2017 Jun 29.

PMID:
28663439
6.

VoroMQA: Assessment of protein structure quality using interatomic contact areas.

Olechnovič K, Venclovas Č.

Proteins. 2017 Jun;85(6):1131-1145. doi: 10.1002/prot.25278. Epub 2017 Mar 24.

PMID:
28263393
7.

A structure-function analysis of the yeast Elg1 protein reveals the importance of PCNA unloading in genome stability maintenance.

Shemesh K, Sebesta M, Pacesa M, Sau S, Bronstein A, Parnas O, Liefshitz B, Venclovas C, Krejci L, Kupiec M.

Nucleic Acids Res. 2017 Apr 7;45(6):3189-3203. doi: 10.1093/nar/gkw1348.

8.

The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures.

Dapkunas J, Timinskas A, Olechnovic K, Margelevicius M, Diciunas R, Venclovas C.

Bioinformatics. 2017 Mar 15;33(6):935-937. doi: 10.1093/bioinformatics/btw756.

PMID:
28011769
9.

Type III CRISPR-Cas Immunity: Major Differences Brushed Aside.

Tamulaitis G, Venclovas Č, Siksnys V.

Trends Microbiol. 2017 Jan;25(1):49-61. doi: 10.1016/j.tim.2016.09.012. Epub 2016 Oct 20. Review.

PMID:
27773522
10.

The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes.

Kazlauskas D, Krupovic M, Venclovas Č.

Nucleic Acids Res. 2016 Jun 2;44(10):4551-64. doi: 10.1093/nar/gkw322. Epub 2016 Apr 25.

11.

Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition.

Kazlauskiene M, Tamulaitis G, Kostiuk G, Venclovas Č, Siksnys V.

Mol Cell. 2016 Apr 21;62(2):295-306. doi: 10.1016/j.molcel.2016.03.024.

12.

Structure of Csm2 elucidates the relationship between small subunits of CRISPR-Cas effector complexes.

Venclovas Č.

FEBS Lett. 2016 May;590(10):1521-9. doi: 10.1002/1873-3468.12179. Epub 2016 May 5.

13.

Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling.

Achar YJ, Balogh D, Neculai D, Juhasz S, Morocz M, Gali H, Dhe-Paganon S, Venclovas Č, Haracska L.

Nucleic Acids Res. 2015 Dec 2;43(21):10277-91. doi: 10.1093/nar/gkv896. Epub 2015 Sep 8.

14.

Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins.

Baranauskė S, Mickutė M, Plotnikova A, Finke A, Venclovas Č, Klimašauskas S, Vilkaitis G.

Nucleic Acids Res. 2015 Mar 11;43(5):2802-12. doi: 10.1093/nar/gkv102. Epub 2015 Feb 12.

15.

The cytolytic activity of vaginolysin strictly depends on cholesterol and is potentiated by human CD59.

Zilnyte M, Venclovas Č, Zvirbliene A, Pleckaityte M.

Toxins (Basel). 2015 Jan 13;7(1):110-28. doi: 10.3390/toxins7010110.

16.

Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus.

Tamulaitis G, Kazlauskiene M, Manakova E, Venclovas Č, Nwokeoji AO, Dickman MJ, Horvath P, Siksnys V.

Mol Cell. 2014 Nov 20;56(4):506-17. doi: 10.1016/j.molcel.2014.09.027. Epub 2014 Nov 6.

17.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

Olechnovič K, Venclovas C.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W259-63. doi: 10.1093/nar/gku294. Epub 2014 May 16.

18.

Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase.

Kazlauskas D, Venclovas C.

Bioinformatics. 2014 Aug 1;30(15):2093-7. doi: 10.1093/bioinformatics/btu204. Epub 2014 Apr 18.

PMID:
24747220
19.

The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures.

Olechnovič K, Venclovas C.

Nucleic Acids Res. 2014 May;42(9):5407-15. doi: 10.1093/nar/gku191. Epub 2014 Mar 12.

20.

Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics.

Fang J, Nevin P, Kairys V, Venclovas Č, Engen JR, Beuning PJ.

Structure. 2014 Apr 8;22(4):572-581. doi: 10.1016/j.str.2014.02.001. Epub 2014 Mar 6.

21.

Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls.

Olechnovič K, Venclovas C.

J Comput Chem. 2014 Mar 30;35(8):672-81. doi: 10.1002/jcc.23538. Epub 2014 Feb 12.

PMID:
24523197
22.

Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes.

Timinskas K, Balvočiūtė M, Timinskas A, Venclovas Č.

Nucleic Acids Res. 2014 Feb;42(3):1393-413. doi: 10.1093/nar/gkt900. Epub 2013 Oct 7.

23.

A vitamin B₁₂ transporter in Mycobacterium tuberculosis.

Gopinath K, Venclovas C, Ioerger TR, Sacchettini JC, McKinney JD, Mizrahi V, Warner DF.

Open Biol. 2013 Feb 13;3(2):120175. doi: 10.1098/rsob.120175.

24.

Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses.

Kazlauskas D, Venclovas C.

Bioinformatics. 2012 Dec 15;28(24):3186-90. doi: 10.1093/bioinformatics/bts626. Epub 2012 Oct 24.

25.

CAD-score: a new contact area difference-based function for evaluation of protein structural models.

Olechnovič K, Kulberkytė E, Venclovas C.

Proteins. 2013 Jan;81(1):149-62. doi: 10.1002/prot.24172. Epub 2012 Sep 29.

PMID:
22933340
26.

Structural and functional analysis of rare missense mutations in human chorionic gonadotrophin β-subunit.

Nagirnaja L, Venclovas Č, Rull K, Jonas KC, Peltoketo H, Christiansen OB, Kairys V, Kivi G, Steffensen R, Huhtaniemi IT, Laan M.

Mol Hum Reprod. 2012 Aug;18(8):379-90. doi: 10.1093/molehr/gas018. Epub 2012 May 3.

27.

Methods for sequence-structure alignment.

Venclovas C.

Methods Mol Biol. 2012;857:55-82. doi: 10.1007/978-1-61779-588-6_3. Review.

PMID:
22323217
28.

Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size.

Kazlauskas D, Venclovas C.

Nucleic Acids Res. 2011 Oct;39(19):8291-305. doi: 10.1093/nar/gkr564. Epub 2011 Jul 8.

29.

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 τ subunit.

Timinskas K, Venclovas Č.

FEBS J. 2011 Sep;278(17):3109-18. doi: 10.1111/j.1742-4658.2011.08236.x. Epub 2011 Aug 2.

30.

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.

Olechnovic K, Margelevicius M, Venclovas C.

Bioinformatics. 2011 Mar 1;27(5):723-4. doi: 10.1093/bioinformatics/btq720. Epub 2010 Dec 24.

PMID:
21186248
31.

Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.

Laganeckas M, Margelevicius M, Venclovas C.

Nucleic Acids Res. 2011 Mar;39(4):1187-96. doi: 10.1093/nar/gkq958. Epub 2010 Oct 20.

32.

Thermodynamics of radicicol binding to human Hsp90 alpha and beta isoforms.

Zubrienė A, Gutkowska M, Matulienė J, Chaleckis R, Michailovienė V, Voroncova A, Venclovas C, Zylicz A, Zylicz M, Matulis D.

Biophys Chem. 2010 Nov;152(1-3):153-63. doi: 10.1016/j.bpc.2010.09.003. Epub 2010 Oct 12.

PMID:
20943306
33.

Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis.

Warner DF, Ndwandwe DE, Abrahams GL, Kana BD, Machowski EE, Venclovas C, Mizrahi V.

Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13093-8. doi: 10.1073/pnas.1002614107. Epub 2010 Jul 6.

34.

COMA server for protein distant homology search.

Margelevicius M, Laganeckas M, Venclovas C.

Bioinformatics. 2010 Aug 1;26(15):1905-6. doi: 10.1093/bioinformatics/btq306. Epub 2010 Jun 6.

PMID:
20529888
35.

Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison.

Margelevicius M, Venclovas C.

BMC Bioinformatics. 2010 Feb 17;11:89. doi: 10.1186/1471-2105-11-89.

36.

The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins.

Venclovas C, Margelevicius M.

Proteins. 2009;77 Suppl 9:81-8. doi: 10.1002/prot.22515.

PMID:
19639635
37.

Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit.

McCauley MJ, Shokri L, Sefcikova J, Venclovas C, Beuning PJ, Williams MC.

ACS Chem Biol. 2008 Sep 19;3(9):577-87. doi: 10.1021/cb8001107. Epub 2008 Jul 25.

38.

Re-searcher: a system for recurrent detection of homologous protein sequences.

Repsys V, Margelevicius M, Venclovas C.

BMC Bioinformatics. 2008 Jun 27;9:296. doi: 10.1186/1471-2105-9-296.

39.

Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains.

Jurenaite-Urbanaviciene S, Serksnaite J, Kriukiene E, Giedriene J, Venclovas C, Lubys A.

Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10358-63. Epub 2007 Jun 6.

40.

Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.

Sukackaite R, Lagunavicius A, Stankevicius K, Urbanke C, Venclovas C, Siksnys V.

Nucleic Acids Res. 2007;35(7):2377-89. Epub 2007 Mar 28.

41.

Physical and functional interactions between MutY glycosylase homologue (MYH) and checkpoint proteins Rad9-Rad1-Hus1.

Shi G, Chang DY, Cheng CC, Guan X, Venclovas C, Lu AL.

Biochem J. 2006 Nov 15;400(1):53-62.

42.

DNA sliding clamps: just the right twist to load onto DNA.

Barsky D, Venclovas C.

Curr Biol. 2005 Dec 20;15(24):R989-92. Review.

43.

Progress over the first decade of CASP experiments.

Kryshtafovych A, Venclovas C, Fidelis K, Moult J.

Proteins. 2005;61 Suppl 7:225-36.

PMID:
16187365
44.
45.
46.

HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.

Daujotyte D, Serva S, Vilkaitis G, Merkiene E, Venclovas C, Klimasauskas S.

Structure. 2004 Jun;12(6):1047-55.

47.

Sequence-structure mapping errors in the PDB: OB-fold domains.

Venclovas C, Ginalski K, Kang C.

Protein Sci. 2004 Jun;13(6):1594-602. Epub 2004 May 7.

48.

Assessment of progress over the CASP experiments.

Venclovas C, Zemla A, Fidelis K, Moult J.

Proteins. 2003;53 Suppl 6:585-95.

PMID:
14579350
49.
50.

Selection and characterization of anti-MUC-1 scFvs intended for targeted therapy.

Winthrop MD, DeNardo SJ, Albrecht H, Mirick GR, Kroger LA, Lamborn KR, Venclovas C, Colvin ME, Burke PA, DeNardo GL.

Clin Cancer Res. 2003 Sep 1;9(10 Pt 2):3845S-53S.

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