P. Zielenkiewicz

发表

The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression*

A. Kierzek, J. Zaim, P. Zielenkiewicz, 2001, The Journal of Biological Chemistry.

P. Zielenkiewicz, S. Kaczanowski, 2010 .

Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data.

P. Zielenkiewicz, P. Pawłowski, 2013, Acta biochimica Polonica.

A Global Review on Short Peptides: Frontiers and Perspectives

Elham Mousavinezhad Sarasia, V. Apostolopoulos, K. Parang, 2021, Molecules.

Lattice simulations of protein crystal formation.

A. Kierzek, P. Pokarowski, P. Zielenkiewicz, 1999, Biophysical chemistry.

Overrepresentation of interactions between homologous proteins in interactomes

P. Zielenkiewicz, S. Kaczanowski, Jerzy Orlowski, 2007, FEBS letters.

A kinetic model of the evolution of a protein interaction network

P. Zielenkiewicz, S. Kaczanowski, P. Pawłowski, 2013, BMC Genomics.

Global analysis of gene expression in maize leaves treated with low temperature: I. Moderate chilling (14 °C)

P. Zielenkiewicz, M. Skoneczny, P. Sowiński, 2009 .

Electrostatic potential of B-DNA: effect of interionic correlations.

P. Zielenkiewicz, S. Gavryushov, P Zielenkiewicz, 1998, Biophysical journal.

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis1[OPEN]

K. Ginalski, P. Zielenkiewicz, B. Wilczyński, 2015, Plant Physiology.

In Silico Identification of Plant miRNAs in Mammalian Breast Milk Exosomes – A Small Step Forward?

P. Zielenkiewicz, A. Lukasik, 2014, PloS one.

Protein-protein recognition: method for finding complementary surfaces of interacting proteins.

P. Zielenkiewicz, P Zielenkiewicz, A Rabczenko, 1984, Journal of theoretical biology.

Searching for interacting surfaces of proteins--the improved method.

P. Zielenkiewicz, A. Rabczenko, 1985, Journal of theoretical biology.

Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study.

Piotr Zielenkiewicz, Grzegorz Wieczorek, P. Zielenkiewicz, 2008, Biophysical journal.

Dominance from the perspective of gene–gene and gene–chemical interactions

P. Zielenkiewicz, S. Kaczanowski, A. Gładki, 2015, Genetica.

Establishment and functional validation of a structural homology model for human DNA methyltransferase 1.

Ralf Schirrmacher, Frank Lyko, Piotr Zielenkiewicz, 2003, Biochemical and biophysical research communications.

Molecular modelling approaches for cystic fibrosis transmembrane conductance regulator studies.

P. Zielenkiewicz, Norbert Odolczyk, 2014, The international journal of biochemistry & cell biology.

Supplemental Text S 1

P. Zielenkiewicz, T. Wyszomirski, M. Siwiak, 2016 .

Transimulation - Protein Biosynthesis Web Service

P. Zielenkiewicz, M. Siwiak, 2013, PloS one.

Potential role of plant miRNAs in the pathogenesis of autosomal dominant polycystic kidney disease: An in silico study.

P. Zielenkiewicz, L. Pączek, M. Niemczyk, 2021, Polish archives of internal medicine.

High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves

P. Zielenkiewicz, L. Pączek, Z. Szweykowska-Kulinska, 2013, BMC Genomics.

Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp

P. Zielenkiewicz, A. Lukasik, M. Reichert, 2019, BMC Genomics.

Databases and ontologies Tools 4 miRs – one place to gather all the tools for miRNA analysis

P. Zielenkiewicz, A. Lukasik, W. Maciej, 2016 .

Biochemical kinetics in changing volumes.

P. Zielenkiewicz, P. Pawłowski, 2004, Acta biochimica Polonica.

Co-regulation of translation in protein

P. Zielenkiewicz, 2015 .

Atherosclerosis Pathways are Activated in Pericoronary Adipose Tissue of Patients with Coronary Artery Disease

P. Zielenkiewicz, Marta Koblowska, R. Iwanicka-Nowicka, 2021, Journal of inflammation research.

Plant chromatin — Learning fromsimilarities and differences

P. Zielenkiewicz, S. Kaczanowski, A. Jerzmanowski, 2003 .

Simulations of nucleation and early growth stages of protein crystals.

A. Kierzek, P. Zielenkiewicz, W. M. Wolf, 1997, Biophysical journal.

Multivalent Ion Distribution around a Cylindrical Polyion: Contribution of Polarization Effects Due to Difference between Dielectric Properties of the Macromolecule's Interior and the Aqueous Solvent

P. Zielenkiewicz, Sergei Gavryushov and, 1997 .

Evaluation of thermodynamic functions relative to cavity formation in aqueous solutions

P. Zielenkiewicz, W. Zielenkiewicz, P. V. Lapshov, 1995 .

Running title: Linker histones in plant adaptation to stress

K. Ginalski, P. Zielenkiewicz, B. Wilczyński, 2015 .

Copper Does Not Induce Tenogenic Differentiation but Promotes Migration and Increases Lysyl Oxidase Activity in Adipose-Derived Mesenchymal Stromal Cells

P. Zielenkiewicz, L. Pączek, K. Zielniok, 2020, Stem cells international.

Evidence for rapid association-dissociation of ribonuclease T1 from a recombinant strain of Escherichia coli.

W. Saenger, P. Zielenkiewicz, Y. Georgalis, 1989, Journal of molecular biology.

Dominance from the perspective of gene–gene and gene–chemical interactions

P. Zielenkiewicz, S. Kaczanowski, A. Gładki, 2015, Genetica.

Improvement of native structure-based peptides as efficient inhibitors of protein-protein interactions of SARS-CoV-2 spike protein and human ACE2

P. Zielenkiewicz, E. Szołajska, U. Zielenkiewicz, 2022, Frontiers in Molecular Biosciences.

Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases.

Frank Lyko, Piotr Zielenkiewicz, Pawel Siedlecki, 2005, Cancer research.

The evolutionary rate of antibacterial drug targets

Piotr Zielenkiewicz, Pawel Szczesny, Szymon Kaczanowski, 2013, BMC Bioinformatics.

Double selective synthetic approach to the N-functionalized 1,4,7-triazacyclononane derivatives: chelating compounds for controllable protein orientation.

P. Zielenkiewicz, Tomasz D Sobieściak, 2010, The Journal of organic chemistry.

New Advances in Short Peptides: Looking Forward

Jillian E. Smith-Carpenter, V. Apostolopoulos, P. Zielenkiewicz, 2022, Molecules.

Discovery of two novel, small-molecule inhibitors of DNA methylation.

Frank Lyko, Piotr Zielenkiewicz, Pawel Siedlecki, 2006, Journal of medicinal chemistry.

The basal transcription factors TBP and TFB from the mesophilic archaeon Methanosarcina mazeii: structure and conformational changes upon interaction with stress-gene promoters.

P. Zielenkiewicz, S. Kaczanowski, E. Conway de Macario, 2001, Journal of molecular biology.

Using tetrahedral grid-based protein models in docking

Piotr Zielenkiewicz, Grzegorz Wieczorek, P. Zielenkiewicz, 2007 .

Prediction of characteristics of interactions of miRNA with mRNA of GRAS, ERF, C2H2 genes of A. thaliana, O. sativa and Z. mays

P. Zielenkiewicz, A. Ivashchenko, K. Uteulin, 2021, Current Plant Biology.

Development and evaluation of a deep learning model for protein-ligand binding affinity prediction

Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki, 2017, 1712.07042.

Molecular dynamics simulation of the hydration shell of a B-DNA decamer reveals two main types of minor-groove hydration depending on groove width.

V. P. Chuprina, U Heinemann, R. Dickerson, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Tools4miRs – one place to gather all the tools for miRNA analysis

Piotr Zielenkiewicz, Anna Lukasik, Maciej Wójcikowski, 2016, Bioinform..

Detection of Plant miRNAs Abundance in Human Breast Milk

P. Zielenkiewicz, U. Zielenkiewicz, A. Lukasik, 2017, International journal of molecular sciences.

Plant MicroRNAs—Novel Players in Natural Medicine?

P. Zielenkiewicz, A. Lukasik, Anna Lukasik, 2016, International journal of molecular sciences.

A Comprehensive, Quantitative, and Genome-Wide Model of Translation

Piotr Zielenkiewicz, Marlena Siwiak, P. Zielenkiewicz, 2010, PLoS Comput. Biol..

Are controversies in science driven by randomness and misbeliefs

P. Zielenkiewicz, T. Wyszomirski, M. Siwiak, 2016 .

e-LiSe - an online tool for finding needles in the "(Medline) haystack"

Piotr Zielenkiewicz, Pawel Siedlecki, Szymon Kaczanowski, 2008, Bioinform..

Design of crotoxin-based peptides with potentiator activity targeting the ΔF508NBD1 Cystic Fibrosis Transmembrane Conductance Regulator.

P. Corringer, G. Lukács, P. Zielenkiewicz, 2022, Journal of molecular biology.

An Overview of miRNA and miRNA Target Analysis Tools.

Anna Lukasik, Piotr Zielenkiewicz, P. Zielenkiewicz, 2019, Methods in molecular biology.

Self-association of bovine pancreatic trypsin inhibitor: specific or nonspecific?

W. Saenger, P. Zielenkiewicz, Y. Georgalis, 1991, Biopolymers.

Methods of molecular modelling of protein-protein interactions.

P. Zielenkiewicz, P Zielenkiewicz, A Rabczenko, 1988, Biophysical chemistry.

Novel calcineurin A (PPP3CA) variant associated with epilepsy, constitutive enzyme activation and downregulation of protein expression

T. Creamer, R. Płoski, M. Wiweger, 2018, European Journal of Human Genetics.

Urine proteomes of healthy aging humans reveal extracellular matrix (ECM) alterations and immune system dysfunction

P. Zielenkiewicz, L. Pączek, M. Dadlez, 2013, AGE.

Theoretical model of reticulocyte to erythrocyte shape transformation.

P. Zielenkiewicz, P. Pawłowski, B. Burzyńska, 2006, Journal of theoretical biology.

Co-regulation of translation in protein complexes

P. Zielenkiewicz, M. Siwiak, 2015, Biology Direct.

Mapping Protein–Protein Interactions of the Resistance-Related Bacterial Zeta Toxin–Epsilon Antitoxin Complex (ε2ζ2) with High Affinity Peptide Ligands Using Fluorescence Polarization

P. Zielenkiewicz, J. Rademann, M. I. Fernández-Bachiller, 2016, Toxins.

Mammalian DNA methyltransferases.

P. Zielenkiewicz, P. Siedlecki, 2006, Acta biochimica Polonica.

The clinical response to vemurafenib in a patient with a rare BRAFV600DK601del mutation-positive melanoma

P. Zielenkiewicz, H. Sevestre, A. Régnier, 2014, BMC Cancer.

The Anti-Inflammatory Effect of Cabbage Leaves Explained by the Influence of bol-miRNA172a on FAN Expression

P. Zielenkiewicz, L. Pączek, K. Kasarełło, 2022, Frontiers in Pharmacology.

DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores

Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki, 2017, Molecules.

Discovery of novel potent ΔF508-CFTR correctors that target the nucleotide binding domain

Piotr Zielenkiewicz, Grzegorz Wieczorek, Michal Dadlez, 2013, EMBO molecular medicine.

54) COMPOUNDS AS MODULATORS OF A MUTANT CFTR PROTEIN AND THEIR USE FOR TREATING DISEASES ASSOCIATED WITH CFTR PROTEIN MALFUNCTION

P. Zielenkiewicz, A. Edelman, G. Wieczorek, 2013 .

Improving detection of protein-ligand binding sites with 3D segmentation

Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki, 2019, Scientific Reports.

Residue solvent accessibilities in the unfolded polypeptide chain.

W. Saenger, P. Zielenkiewicz, 1992, Biophysical journal.

EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology

Ursula Bilitewski, Aigars Jirgensons, Jordi Mestres, 2019, SLAS discovery : advancing life sciences R & D.

Models of protein crystal growth.

A. Kierzek, P. Zielenkiewicz, A M Kierzek, 2001, Biophysical chemistry.

3-Methyladenine-DNA glycosylase I from Escherichia coli-computer modeling and supporting experimental evidence.

A. Kierzek, P. Zielenkiewicz, B. Tudek, 2000, Biochemical and biophysical research communications.

Native Structure-Based Peptides as Potential Protein–Protein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor

P. Zielenkiewicz, J. Poznański, E. Marzec, 2021, Molecules.

Theoretical model of thalassemic erythrocyte shape transformation.

P. Zielenkiewicz, P. Pawłowski, B. Burzyńska, 2008, Journal of theoretical biology.

Proteins contribute insignificantly to the intrinsic buffering capacity of yeast cytoplasm.

P. Zielenkiewicz, L. Pączek, J. Poznański, 2013, Biochemical and biophysical research communications.

Nicotiana tabacum Osmotic Stress-activated Kinase Is Regulated by Phosphorylation on Ser-154 and Ser-158 in the Kinase Activation Loop*

P. Zielenkiewicz, M. Dadlez, P. Siedlecki, 2006, Journal of Biological Chemistry.

Urine proteomes of healthy aging humans reveal extracellular matrix (ECM) alterations and immune system dysfunction

P. Zielenkiewicz, L. Pączek, M. Dadlez, 2013, AGE.

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

Marta M. Stepniewska-Dziubinska, Pawel Siedlecki, Piotr Zielenkiewicz, 2017, Bioinform..

Structural models of CFTR–AMPK and CFTR–PKA interactions: R-domain flexibility is a key factor in CFTR regulation

P. Zielenkiewicz, A. Edelman, M. Siwiak, 2011, Journal of Molecular Modeling.

Comparison of two different lysozyme types under native and crystallization conditions using two-dimensional NMR and dynamic light scattering.

W. Saenger, P. Zielenkiewicz, J. Poznański, 2003, Biophysical chemistry.

Microscopic model of protein crystal growth.

A. Kierzek, P. Pokarowski, P. Zielenkiewicz, 2000, Biophysical chemistry.

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field

Piotr Zielenkiewicz, Pawel Siedlecki, Maciej Wójcikowski, 2015, Journal of Cheminformatics.

Arteriovenous oscillations of the redox potential: Is the redox state influencing blood flow?

P. Zielenkiewicz, L. Pączek, J. Poznański, 2017, Redox report : communications in free radical research.

The formation of protein secondary structure. Its connection with amino acid sequence.

P. Zielenkiewicz, D. Płochocka, A. Rabczenko, 1988, Biophysical chemistry.

Hypophosphatemia and sudden infant death syndrome (SIDS)—is ATP the link?

P. Zielenkiewicz, L. Pączek, J. Poznański, 2014, Upsala journal of medical sciences.

Structurally conserved water molecules in ribonuclease T1.

W. Saenger, P. Zielenkiewicz, R. Malin, 1991, The Journal of biological chemistry.

Rattlesnake Phospholipase A2 Increases CFTR-Chloride Channel Current and Corrects ∆F508CFTR Dysfunction: Impact in Cystic Fibrosis.

P. Corringer, G. Lukács, F. Saul, 2016, Journal of molecular biology.

Systemic bis-phosphinic acid derivative restores chloride transport in Cystic Fibrosis mice

J. Jais, C. Schreiweis, S. Moriceau, 2022, Scientific Reports.

Supramolecular synthon hierarchy in cyclopropyl-containing peptide-derived compounds

P. Zielenkiewicz, J. Bojarska, K. Kaczmarek, 2022, CrystEngComm.

Endogenous piRNAs Can Interact with the Omicron Variant of the SARS-CoV-2 Genome

P. Zielenkiewicz, A. Ivashchenko, A. Kondybayeva, 2023, Current issues in molecular biology.

DeltaF508 mutation increases conformational flexibility of CFTR protein.

P. Zielenkiewicz, P Zielenkiewicz, G. Wieczorek, 2008, Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society.

The role of structural biology in pandemic's puzzles: amino acids and short peptides as key players

P. Zielenkiewicz, J. Feehan, J. Bojarska, 2021, Acta Crystallographica Section A: Foundations and Advances.

Non-specific clustering of histidine tagged green fluorescent protein mediated by surface interactions: the collective effect in the protein-adsorption behaviour

P. Zielenkiewicz, Tomasz D Sobieściak, 2013 .

Interactions of piRNAs with the mRNA of Candidate Genes in Esophageal Squamous Cell Carcinoma

P. Zielenkiewicz, A. Ivashchenko, M. Tauassarova, 2023, Current Issues in Molecular Biology.

The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words

Piotr Zielenkiewicz, Pawel Siedlecki, Szymon Kaczanowski, 2009, BMC Bioinformatics.

Stress-Induced Phosphaturia in Weaned Piglets

P. Zielenkiewicz, Z. Gajewski, Paweł Szczęsny, 2020, Animals : an open access journal from MDPI.

Improving detection of protein-ligand binding sites with 3D segmentation

Marta M. Stepniewska-Dziubinska, P. Zielenkiewicz, P. Siedlecki, 2019, Scientific Reports.

EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology

J. Mestres, S. Krauss, J. Brea, 2019, SLAS discovery : advancing life sciences R & D.

Using Machine Learning in Accuracy Assessment of Knowledge-Based Energy and Frequency Base Likelihood in Protein Structures

Dimitar Vassilev, Iliyan Mihaylov, Piotr Zielenkiewicz, 2020, ICCS.

Tertiary structure of RNase Pch1 predicted from the model structure of RNase Ms and the crystal structure of RNase T1

W. Saenger, P. Zielenkiewicz, R. Floegel, 1990, European Biophysics Journal.

Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp

P. Zielenkiewicz, A. Lukasik, M. Reichert, 2019, BMC Genomics.

Co-regulation of translation in protein complexes

P. Zielenkiewicz, M. Siwiak, 2015, Biology Direct.

Protein Interaction Network. Double Exponential Model

Piotr Pawlowski, Szymon Kaczanowski, Piotr Zielenkiewicz, 2008 .

Molecular modelling approaches for cystic fibrosis transmembrane conductance regulator studies.

P. Zielenkiewicz, Norbert Odolczyk, 2014, The international journal of biochemistry & cell biology.

Rattlesnake Phospholipase A2 Increases CFTR-Chloride Channel Current and Corrects ∆F508CFTR Dysfunction: Impact in Cystic Fibrosis.

P. Corringer, G. Lukács, F. Saul, 2016, Journal of molecular biology.

Novel calcineurin A (PPP3CA) variant associated with epilepsy, constitutive enzyme activation and downregulation of protein expression

T. Creamer, R. Płoski, M. Wiweger, 2018, European Journal of Human Genetics.

DiSCuS: An Open Platform for (Not Only) Virtual Screening Results Management

Piotr Zielenkiewicz, Pawel Siedlecki, Maciej Wójcikowski, 2014, J. Chem. Inf. Model..

Pafnucy - A deep neural network for structure-based drug discovery pdf

Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki, 2017, ArXiv.

Abundant Plpp Sequence Has the Same Conformation in Unrelated Proteins

P. Zielenkiewicz, D. Płochocka, 1995, Protein & Peptide Letters.