Č. Venclovas

发表

A modified definition of Sov, a segment‐based measure for protein secondary structure prediction assessment

B. Rost, A. Zemla, Č. Venclovas, 1999, Proteins.

Molecular modeling‐based analysis of interactions in the RFC‐dependent clamp‐loading process

Č. Venclovas, M. Colvin, M. Thelen, 2002, Protein science : a publication of the Protein Society.

Comparative modeling in CASP6 using consensus approach to template selection, sequence‐structure alignment, and structure assessment

Č. Venclovas, Mindaugas Margelevičius, 2005, Proteins.

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

Č. Venclovas, V. Mizrahi, B. Kana, 2010, Proceedings of the National Academy of Sciences.

Addressing the issue of sequence‐to‐structure alignments in comparative modeling of CASP3 target proteins

Krzysztof Fidelis, Česlovas Venclovas, Krzysztof Ginalski, 1999, Proteins.

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

Č. Venclovas, M. Krupovic, D. Kazlauskas, 2016, Nucleic acids research.

Distinct Double- and Single-Stranded DNA Binding of E. coli Replicative DNA Polymerase III α Subunit

Č. Venclovas, Leila Shokri, Mark C. Williams, 2008, ACS chemical biology.

Sequence‐structure mapping errors in the PDB: OB‐fold domains

Ceslovas Venclovas, Krzysztof Ginalski, Č. Venclovas, 2004, Protein science : a publication of the Protein Society.

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

Č. Venclovas, Edita Kriukienė, S. Jurenaite-Urbanaviciene, 2007, Proceedings of the National Academy of Sciences.

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

Č. Venclovas, V. Šikšnys, C. Urbanke, 2007, Nucleic acids research.

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

Č. Venclovas, V. Šikšnys, M. Szczelkun, 2018, Nucleic acids research.

Estimation of model accuracy in CASP13

Arne Elofsson, Karolis Uziela, Björn Wallner, 2019, Proteins.

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

Č. Venclovas, D. Kazlauskas, Darius Kazlauskas, 2011, Nucleic acids research.

COMA server for protein distant homology search

Mindaugas Margelevicius, Ceslovas Venclovas, Mindaugas Laganeckas, 2010, Bioinform..

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

Č. Venclovas, Mindaugas Margelevičius, Mindaugas Laganeckas, 2010, Nucleic acids research.

New insights into the structures and interactions of bacterial Y-family DNA polymerases

Č. Venclovas, Kęstutis Timinskas, 2019, Nucleic acids research.

The path of a protein chain can be approximated by the conformation dictated by interpeptide ionic bridges

Č. Venclovas, V. Lim, N. Kurochkina, 1992, FEBS letters.

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

Č. Venclovas, S. Klimašauskas, G. Vilkaitis, 2004, Structure.

Selection and Characterization of Anti-MUC-1 scFvs Intended for Targeted Therapy 1

Č. Venclovas, K. Lamborn, G. Denardo, 2003 .

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

Č. Venclovas, K. Lamborn, G. Denardo, 2003, Clinical cancer research : an official journal of the American Association for Cancer Research.

Diversity and evolution of B-family DNA polymerases

Č. Venclovas, P. Forterre, M. Krupovic, 2020, Nucleic acids research.

Genome Replication of Bacterial and Archaeal Viruses

Č. Venclovas, 2019 .

Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense.

Ayal B. Gussow, E. Koonin, Y. Wolf, 2020, Nucleic acids research.

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

Č. Venclovas, O. Christiansen, R. Steffensen, 2012, Molecular human reproduction.

SURVEY AND SUMMARY Evolutionary and functional classiﬁcation of the CARF domain superfamily, key sensors in prokaryotic antivirus defense

Ayal B. Gussow, E. Koonin, Y. Wolf, 2020 .

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

Szilvia Juhász, Č. Venclovas, Himabindu Gali, 2015, Nucleic acids research.

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

Č. Venclovas, Kęstutis Timinskas, 2011, The FEBS journal.

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 s subunit

Č. Venclovas, Kęstutis Timinskas, 2011 .

Five‐stranded β‐sheet sandwiched with two α‐helices: A structural link between restriction endonucleases EcoRI and EcoRV

Č. Venclovas, V. Šikšnys, A. Timinskas, 1994 .

A vitamin B12 transporter in Mycobacterium tuberculosis

Č. Venclovas, J. Sacchettini, T. Ioerger, 2013, Open Biology.

Different enzymes with similar structures involved in Mg2+-mediated polynucleotidyl transfer

Č. Venclovas, V. Šikšnys, 1995, Nature Structural Biology.

Assessment of progress over the CASP experiments

Ceslovas Venclovas, Krzysztof Fidelis, John Moult, 2003, Proteins.

NR5A1 c.991‐1G > C splice‐site variant causes familial 46,XY partial gonadal dysgenesis with incomplete penetrance

Č. Venclovas, T. Lenaerts, M. Punab, 2020, Clinical endocrinology.

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

Česlovas Venclovas, Gintautas Tamulaitis, Virginijus Siksnys, 2017, Trends in microbiology.

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

Česlovas Venclovas, Gintautas Tamulaitis, Virginijus Siksnys, 2016, Molecular cell.

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

Česlovas Venclovas, Gintautas Tamulaitis, Virginijus Siksnys, 2017, Science.

The Cytolytic Activity of Vaginolysin Strictly Depends on Cholesterol and Is Potentiated by Human CD59

Č. Venclovas, M. Pleckaityte, A. Zvirbliene, 2015, Toxins.

How are tRNAs and mRNA arranged in the ribosome? An attempt to correlate the stereochemistry of the tRNA-mRNA interaction with constraints imposed by the ribosomal topography.

A. Spirin, Č. Venclovas, V. Lim, 1992, Nucleic acids research.

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

Č. Venclovas, O. Christiansen, R. Steffensen, 2012 .

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

Č. Venclovas, M. Kupiec, Oren Parnas, 2017, Nucleic acids research.

Template-Based Modeling of Protein Complexes Using the PPI3D Web Server.

Česlovas Venclovas, Justas Dapkūnas, Č. Venclovas, 2020, Methods in molecular biology.

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

Mindaugas Margelevicius, Ceslovas Venclovas, Č. Venclovas, 2010, BMC Bioinformatics.

Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease

Č. Venclovas, V. Šikšnys, D. Kazlauskas, 2021, Nature.

PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage

Č. Venclovas, Zhenglin Hou, V. Šikšnys, 2020, Nucleic acids research.

PAM recognition by miniature CRISPR-Cas14 triggers programmable double-stranded DNA cleavage

Č. Venclovas, Zhenglin Hou, V. Šikšnys, 2019, bioRxiv.

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

Č. Venclovas, 2016, FEBS letters.

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Stan J. J. Brouns, Omer S. Alkhnbashi, Shiraz A. Shah, 2019, Nature Reviews Microbiology.

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

Ceslovas Venclovas, Philippe Horvath, Gintautas Tamulaitis, 2014, Molecular cell.

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

Č. Venclovas, Monika Balvociute, A. Timinskas, 2013, Nucleic acids research.

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

Č. Venclovas, S. Klimašauskas, G. Vilkaitis, 2015, Nucleic acids research.

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

Č. Venclovas, C. Cheng, A. Lu, 2006, The Biochemical journal.

Physical and functional interactions between MutY glycosylase homologue ( MYH ) and checkpoint proteins Rad 9 – Rad 1 – Hus 1

Č. Venclovas, C. Cheng, D. Chang, 2006 .

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

Č. Venclovas, R. Sorek, V. Šikšnys, 2021, bioRxiv.

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Rolf Backofen, Philippe Horvath, Rodolphe Barrangou, 2019, Nature Reviews Microbiology.

Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment

Č. Venclovas, K. Fidelis, J. Moult, 2021, Proteins.

Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes

Ceslovas Venclovas, Michael P. Thelen, Č. Venclovas, 2000, Nucleic Acids Res..

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

Ceslovas Venclovas, Darius Kazlauskas, Č. Venclovas, 2012, Bioinform..

Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease

Č. Venclovas, V. Šikšnys, D. Kazlauskas, 2021, Nature.

A catalogue of biochemically diverse CRISPR-Cas9 orthologs

Joshua K Young, Clara M Alarcon, Č. Venclovas, 2020, Nature Communications.

Comparative analysis of methods for evaluation of protein models against native structures

Kliment Olechnovic, Ceslovas Venclovas, Andriy Kryshtafovych, 2018, Bioinform..

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Jeffrey J. Gray, Panagiotis I. Koukos, Johnathan D. Guest, 2021, Proteins.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

How Proteins Slide on DNA

Č. Venclovas, T. Laurence, D. Barsky, 2010 .

Prediction of protein assemblies by structure sampling followed by interface-focused scoring

Č. Venclovas, J. Dapkūnas, Kliment Olechnovič, 2023, bioRxiv.

A Sliding Clamp Model for the Rad1 Family of Cell Cycle Checkpoint Proteins

Č. Venclovas, K. Fidelis, M. Thelen, 1999, Cell.

Biochemically diverse CRISPR-Cas9 orthologs

Clara M Alarcon, Č. Venclovas, Zhenglin Hou, 2020, bioRxiv.

VoroMQA: Assessment of protein structure quality using interatomic contact areas

Kliment Olechnovič, Česlovas Venclovas, Č. Venclovas, 2017, Proteins.

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

Č. Venclovas, P. Forterre, M. Krupovic, 2017, Journal of molecular biology.

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

Ceslovas Venclovas, Darius Kazlauskas, Č. Venclovas, 2014, Bioinform..

Processing and analysis of CASP3 protein structure predictions

C Venclovas, A Zemla, K Fidelis, 1999, Proteins.

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

Č. Venclovas, V. Kairys, P. Beuning, 2014, Structure.

Progress over the first decade of CASP experiments

Ceslovas Venclovas, Krzysztof Fidelis, Andriy Kryshtafovych, 2005, Proteins.

DNA Sliding Clamps: Just the Right Twist to Load onto DNA

Č. Venclovas, D. Barsky, 2005, Current Biology.

Comparison of performance in successive CASP experiments

C Venclovas, A Zemla, K Fidelis, 2001, Proteins.

HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.

Č. Venclovas, V. Šikšnys, G. Sasnauskas, 2020, Molecular cell.

RecA-NT homology motif in ImuB is essential for mycobacterial ImuA’-ImuB protein interaction and mutasome function

Č. Venclovas, M. Lamers, D. Warner, 2023, bioRxiv.

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

Č. Venclovas, M. Gutkowska, M. Żylicz, 2010, Biophysical chemistry.

Structure‐based sequence alignment for the β‐trefoil subdomain of the clostridial neurotoxin family provides residue level information about the putative ganglioside binding site

Č. Venclovas, K. Fidelis, K. Ginalski, 2000, FEBS letters.

CAD‐score: A new contact area difference‐based function for evaluation of protein structural models

Kliment Olechnovič, Eleonora Kulberkytė, Ceslovas Venclovas, 2013, Proteins.

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

Č. Venclovas, G. Gasiunas, V. Šikšnys, 2018, EMBO reports.

TnpB structure reveals minimal functional core of Cas12 nuclease family

Č. Venclovas, G. Montoya, V. Šikšnys, 2023, Nature.

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

Charles W Christoffer, H. Wolfson, O. Schueler‐Furman, 2023, Proteomics.

Template‐based modeling of diverse protein interactions in CAPRI rounds 38‐45

Kliment Olechnovič, Česlovas Venclovas, Visvaldas Kairys, 2019, Proteins.

Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV.

Č. Venclovas, V. Šikšnys, A. Timinskas, 1994, Proteins.

Processing and evaluation of predictions in CASP4

Krzysztof Fidelis, John Moult, Adam Zemla, 2001, Proteins.

VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes

Kliment Olechnovic, Ceslovas Venclovas, Č. Venclovas, 2019, Nucleic Acids Res..

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

Kliment Olechnovic, Ceslovas Venclovas, Č. Venclovas, 2014, J. Comput. Chem..

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

Kliment Olechnovič, Česlovas Venclovas, Justas Dapkūnas, 2018, Proteins.

FY05 LDRD Fianl Report Investigation of AAA+ protein machines that participate in DNA replication, recombination, and in response to DNA damage LDRD Project Tracking Code: 04-LW-049

Č. Venclovas, D. Sawicka, D. Barsky, 2006 .

VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures

Kliment Olechnovic, Sergei Grudinin, Ilia Igashov, 2020, bioRxiv.

Comparative modeling of CASP4 target proteins: Combining results of sequence search with three‐dimensional structure assessment

C Venclovas, Č. Venclovas, 2001, Proteins.

Numerical criteria for the evaluation of ab initio predictions of protein structure

C Venclovas, A Zemla, K Fidelis, 1997, Proteins.

PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

Mindaugas Margelevicius, Ceslovas Venclovas, Č. Venclovas, 2005, BMC Bioinformatics.

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

Česlovas Venclovas, Mindaugas Margelevičius, Č. Venclovas, 2009, Proteins.

Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction

Kliment Olechnovič, Česlovas Venclovas, Justas Dapkunas, 2021, Proteins.

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

Kliment Olechnovic, Ceslovas Venclovas, Č. Venclovas, 2014, Nucleic Acids Res..

Viral DNA replication: new insights and discoveries from large scale computational analysis

Č. Venclovas, Darius Kazlauskas, 2015, BMC Bioinformatics.

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

Kliment Olechnovic, Mindaugas Margelevicius, Ceslovas Venclovas, 2016, Bioinform..

Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance

Ceslovas Venclovas, Č. Venclovas, 2003, Proteins.

Structural modeling of protein complexes: Current capabilities and challenges

Kliment Olechnovič, Česlovas Venclovas, Justas Dapkūnas, 2019, Proteins.

Criteria for evaluating protein structures derived from comparative modeling

C Venclovas, A Zemla, K Fidelis, 1997, Proteins.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Johnathan D. Guest, Adam K. Sieradzan, Charles W Christoffer, 2023, Proteins.

Investigating the composition and recruitment of the mycobacterial ImuA′–ImuB–DnaE2 mutasome

Č. Venclovas, M. Lamers, R. Woodgate, 2023, eLife.

Sir2-domain associated short prokaryotic Argonautes provide defence against invading mobile genetic elements through NAD+ depletion

Č. Venclovas, R. Sorek, V. Šikšnys, 2022 .

The mycobacterial ImuA’-ImuB-DnaE2 mutasome: 1 composition and recruitment in live cells 2

Č. Venclovas, M. Lamers, R. Woodgate, 2022 .

The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein

Č. Venclovas, G. Sasnauskas, M. Zaremba, 2024, Nucleic acids research.