List of works - Česlovas Venclovas

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 25 October 2019

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

scientific article

COMA server for protein distant homology search

scientific article published on 06 June 2010

Codon-anticodon pairing. A model for interacting codon-anticodon duplexes located at the ribosomal A- and P-sites

scientific article published on November 23, 1992

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

scientific article published on 01 March 2019

Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment.

scientific article

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

scientific article published on 7 October 2013

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

scientific article published on 6 March 2014

Criteria for evaluating protein structures derived from comparative modeling ⬇️

scientific article published on January 1, 1997

Different enzymes with similar structures involved in Mg(2+)-mediated polynucleotidyl transfer

scientific article published on 01 October 1995

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

scientific article published on 11 June 2018

Estimation of model accuracy in CASP13

scientific article published on 16 July 2019

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

scientific article published on 19 December 2019

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

scientific article published on 01 November 1994

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

scientific article published on 12 February 2015

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

scientific article

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

scientific article

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.

scientific article published on June 1992

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

scientific article

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

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

scientific article

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

scientific article

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

scientific article published on 09 December 2020

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

scientific article published on 01 May 2019

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

scientific article published on 30 November 2017

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

scientific article

PPI3D: a web server for searching, analyzing and modeling protein–protein, protein–peptide and protein–nucleic acid interactions

scientific article published in 2024

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

scientific article

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling

scientific article published on 30 November 2023

Some measures of comparative performance in the three CASPs.

scientific article

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

scientific article published on April 2016

Structural modeling of protein complexes: Current capabilities and challenges

scientific article published on 22 July 2019

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

scientific article published on 19 April 2016

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

scientific article published on 01 September 2000

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

scientific article published on 07 November 2019

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

scientific article published on 16 May 2014

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

scientific article published on 20 February 2018

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.

scientific article

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

scientific article published on 22 December 2016

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

scientific article

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

scientific article

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

scientific article published on May 4, 1992

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

scientific article

Type III CRISPR-Cas Immunity: Major Differences Brushed Aside

scientific article

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

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

scientific article published on 01 July 2019

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

scientific article

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

scientific article

List of works by Česlovas Venclovas

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

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

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

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

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

COMA server for protein distant homology search

Codon-anticodon pairing. A model for interacting codon-anticodon duplexes located at the ribosomal A- and P-sites

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

Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment.

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

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

Criteria for evaluating protein structures derived from comparative modeling ⬇️

Different enzymes with similar structures involved in Mg(2+)-mediated polynucleotidyl transfer

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

Estimation of model accuracy in CASP13

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

PPI3D: a web server for searching, analyzing and modeling protein–protein, protein–peptide and protein–nucleic acid interactions

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

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling

Some measures of comparative performance in the three CASPs.

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

Structural modeling of protein complexes: Current capabilities and challenges

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

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

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

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

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

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.

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

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

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

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

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

Type III CRISPR-Cas Immunity: Major Differences Brushed Aside

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

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

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

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