List of works - Krzysztof Ginalski

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

scientific article published on 17 March 2013

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity

scholarly article

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

scientific article published in September 2010

Comparative modeling for protein structure prediction

scientific article

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

scientific article

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human

scientific article

SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family

scientific journal article

A comprehensive update of the sequence and structure classification of kinases

scientific article

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440

scientific article

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.

scientific article published on 6 March 2017

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

scientific article

Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses

scientific article published in April 2003

Detecting distant homology with Meta-BASIC.

scientific article published on July 2004

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

scientific article

Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.

scientific article

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

scientific article published on 23 January 2014

Identification of novel restriction endonuclease-like fold families among hypothetical proteins

scientific article

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification

scientific article

Snf2 proteins in plants: gene silencing and beyond

scientific article published on 09 September 2008

Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade

scientific article published on December 2005

Practical lessons from protein structure prediction

scientific article

Extending the aerolysin family: from bacteria to vertebrates

scientific article

The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast

scientific article

Detection of reliable and unexpected protein fold predictions using 3D-Jury

scientific article

Efficacy of 2-halogen substituted D-glucose analogs in blocking glycolysis and killing "hypoxic tumor cells".

scientific article published on 23 March 2006

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform

scientific article published on 10 April 2015

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome

scientific article

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment

scientific article published on 01 January 2003

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches

scientific article published on 20 June 2007

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis

scientific article (publication date: November 2015)

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

scholarly article by Thomas Clouaire published in September 2018

VoteDock: consensus docking method for prediction of protein-ligand interactions

scientific article

Protein structure prediction for the male-specific region of the human Y chromosome

scientific article

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners

scientific article published in September 2003

Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels

scientific article

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

scientific article

BOF: a novel family of bacterial OB-fold proteins

scientific article

Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding

scientific article

FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases

scientific article

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

scientific article

Application of 3D-Jury, GRDB, and Verify3D in fold recognition

scientific article published on January 2003

Target specific compound identification using a support vector machine

scientific article

Fungal lifestyle reflected in serine protease repertoire

scientific article

Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease

scientific article published in March 2006

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

scientific article

Detailed mechanism of squalene epoxidase inhibition by terbinafine

scientific article published on 13 January 2011

BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases

scientific article

Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily

scientific article published on 15 December 2006

The interactome: Predicting the protein-protein interactions in cells

scientific article published on 6 October 2008

Comprehensive classification of the PIN domain-like superfamily

scientific article

List of works by Krzysztof Ginalski

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Comparative modeling for protein structure prediction

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human

SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family

A comprehensive update of the sequence and structure classification of kinases

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses

Detecting distant homology with Meta-BASIC.

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

Determinants in nuclease specificity of Ape1 and Ape2, human homologues of Escherichia coli exonuclease III.

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Identification of novel restriction endonuclease-like fold families among hypothetical proteins

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification

Snf2 proteins in plants: gene silencing and beyond

Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade

Practical lessons from protein structure prediction

Extending the aerolysin family: from bacteria to vertebrates

The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast

Detection of reliable and unexpected protein fold predictions using 3D-Jury

Efficacy of 2-halogen substituted D-glucose analogs in blocking glycolysis and killing "hypoxic tumor cells".

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

VoteDock: consensus docking method for prediction of protein-ligand interactions

Protein structure prediction for the male-specific region of the human Y chromosome

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners

Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

BOF: a novel family of bacterial OB-fold proteins

Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding

FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

Application of 3D-Jury, GRDB, and Verify3D in fold recognition

Target specific compound identification using a support vector machine

Fungal lifestyle reflected in serine protease repertoire

Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

Detailed mechanism of squalene epoxidase inhibition by terbinafine

BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases

Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily

The interactome: Predicting the protein-protein interactions in cells

Comprehensive classification of the PIN domain-like superfamily